1
|
Xu Z, Wang S, Li R, Li H, Zhang C, Zhang Y, Zhang X, Quan F, Wang F. Enhancement of microbial community dynamics and metabolism in compost through ammonifying cultures inoculation. ENVIRONMENTAL RESEARCH 2024; 255:119188. [PMID: 38795950 DOI: 10.1016/j.envres.2024.119188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/16/2024] [Accepted: 05/19/2024] [Indexed: 05/28/2024]
Abstract
The efficient use of livestock and poultry manure waste has become a global challenge, with microorganisms playing an important role. To investigate the impact of novel ammonifying microorganism cultures (NAMC) on microbial community dynamics and carbon and nitrogen metabolism, five treatments [5% (v/w) sterilized distilled water, Amm-1, Amm-2, Amm-3, and Amm-4] were applied to cow manure compost. Inoculation with NAMC improved the structure of bacterial and fungal communities, enriched the populations of the functional microorganisms, enhanced the role of specific microorganisms, and promoted the formation of tight modularity within the microbial network. Further functional predictions indicated a significant increase in both carbon metabolism (CMB) and nitrogen metabolism (NMB). During the thermophilic phase, inoculated NAMC treatments boosted carbon metabolism annotation by 10.55%-33.87% and nitrogen metabolism annotation by 26.69%-63.11. Structural equation modeling supported the NAMC-mediated enhancement of NMB and CMB. In conclusion, NAMC inoculation, particularly with Amm-4, enhanced the synergistic interaction between bacteria and fungi. This collaboration promoted enzymatic catabolic and synthetic processes, resultng in positive feedback loops with the endogenous microbial community. Understanding these mechanisms not only unravels how ammonifying microorganisms influence microbial communities but also paves the way for the development of the composting industry and global waste management practices.
Collapse
Affiliation(s)
- Zhiming Xu
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Shaowen Wang
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Ronghua Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Huijia Li
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science Technology and Research (A*STAR), 31 Biopolis Way, Level 6 Nanos Building, Singapore 138669, Singapore
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Xiu Zhang
- North Minzu University Ningxia Key Laboratory for the Development and Application of Microbial Resources in Extreme Environments, Yinchuan, 750021, China.
| | - Fusheng Quan
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Yangling, 712100, China.
| | - Faming Wang
- Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Leuven, 3001, Belgium
| |
Collapse
|
2
|
Hu Y, Zhang X, Chen H, Jiang Y, Zhang J. Effects of forest age and season on soil microbial communities in Chinese fir plantations. Microbiol Spectr 2024; 12:e0407523. [PMID: 38980023 PMCID: PMC11302042 DOI: 10.1128/spectrum.04075-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/18/2024] [Indexed: 07/10/2024] Open
Abstract
Understanding changes in the distribution patterns and diversity of soil microbial communities from the perspectives of age-related changes, seasonal variations, and the interaction between the two factors can facilitate the management of plantations. In Chinese fir plantations, we collected soils from different depths in over-mature forests, mature forests, near-mature forests, middle-aged forests, and young forests in summer, autumn, and winter in China's subtropical regions. As the forests developed, bacterial and fungal communities' diversity changed, reached a minimum value at near-mature forests, and then increased in mature forests or over-mature forests. Near-mature forests had the lowest topological properties. The Shannon index of microbial communities varied with seasonal changes (P < 0.05). Bacterial and fungal community composition at genus level was more closely related to temperature indicators (including daily average temperature, daily maximum temperature, and daily minimum temperature) (P < 0.01, 0.5554 < R2 <0.8185) than daily average precipitation (P > 0.05, 0.0321 < R2 <0.6773). Bacteria were clustered by season and fungi were clustered by forest age. We suggested that extending the tree cultivation time of plantations could promote microbial community recovery. In addition, we found some species worthy of attention, including Bacteroidetes in autumn in over-mature forests, and Firmicutes in summer in young forests.IMPORTANCEChinese fir [Cunninghamia lanceolata (Lamb.) Hook] is an important fast-growing species with the largest artificial forest area in China, with the outstanding problems of low quality in soil. Soil microorganisms play a crucial role in soil fertility by decomposing organic matter, optimizing soil structure, and releasing essential nutrients for plant growth. In order to maintain healthy soil quality and prevent nutrient depletion and land degradation, it is crucial to understand the changes of soil microbial composition and diversity. Our study determined to reveal the change of soil microbial community from stand age, season, and the interaction between the two aspects, which is helpful to understand how interannual changes in different years and seasonal changes in one year affect soil fertility restoration and sustainable forest plantation management. It is a meaningful exploration of soil microbial communities and provides new information for further research.
Collapse
Affiliation(s)
- Yuxin Hu
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xiongqing Zhang
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Hanyue Chen
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yihang Jiang
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jianguo Zhang
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| |
Collapse
|
3
|
Liu Y, Bao L, Sun W, Cui Y, Li X, Ji X, Wei Y, Tan Y. Diversity and composition of active and total bacteria in rhizospheric soil in response to continuous cropping years of Panax notoginseng. Folia Microbiol (Praha) 2024; 69:733-745. [PMID: 38038798 DOI: 10.1007/s12223-023-01109-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/12/2023] [Indexed: 12/02/2023]
Abstract
The synchronous research and analysis of total and active soil microbial communities can provide insight into how these communities are impacted by continuous cropping years and pathogen infection. The diversity of total and active bacteria in rhizospheric soil of 2-year-old and 3-year-old healthy and diseased Panax notoginseng can comprehensively reveal the bacterial response characteristics in continuous cropping practice. The results showed that 4916 operational taxonomic units (OTUs) were found in the rhizospheric soil bacterial community of P. notoginseng at the DNA level, but only 2773 OTUs were found at the RNA level. The rhizospheric environment had significant effects on the active and bacterial communities, as indicated by the number of OTUs, Shannon, Chao1, Faith's phylogenetic diversity (Faith's PD), and Simpson's diversity indexes. The DNA level can better show the difference in diversity level before and after infection with root rot. The bacterial Chao1 and Faith's PD diversity indexes of 2-year-old root rot-diseased P. notoginseng rhizospheric soil (D2) were higher than that of healthy plants, while the bacterial Shannon diversity index of 3-year-old root rot-diseased P. notoginseng rhizospheric soil (D3) was the lowest in the total bacteria. Principal coordinate analysis (PCoA) illustrated that the total bacterial species composition changed markedly after root rot disease. There were significant differences in the composition of active bacterial species between the 2-year and 3-year rhizospheres. In conclusion, the total and active edaphic rhizospheric bacterial communities could provide important opportunities to understand the responses of bacteria to continuous cropping of P. notoginseng.
Collapse
Affiliation(s)
- Yuyan Liu
- Faculty of Science, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Limei Bao
- Faculty of Science, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Wanwan Sun
- Faculty of life Science and Technology, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Yinshan Cui
- Faculty of life Science and Technology, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Xiaoran Li
- Faculty of life Science and Technology, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Xiuling Ji
- Faculty of life Science and Technology, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Yunlin Wei
- Faculty of life Science and Technology, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China.
| | - Yong Tan
- Faculty of Science, Kunming University of Science and Technology, No. 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China.
| |
Collapse
|
4
|
Bielčik M, Schlägel UE, Schäfer M, Aguilar-Trigueros CA, Lakovic M, Sosa-Hernández MA, Hammer EC, Jeltsch F, Rillig MC. Aligning spatial ecological theory with the study of clonal organisms: the case of fungal coexistence. Biol Rev Camb Philos Soc 2024. [PMID: 39073180 DOI: 10.1111/brv.13119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024]
Abstract
Established ecological theory has focused on unitary organisms, and thus its concepts have matured into a form that often hinders rather than facilitates the ecological study of modular organisms. Here, we use the example of filamentous fungi to develop concepts that enable integration of non-unitary (modular) organisms into the established community ecology theory, with particular focus on its spatial aspects. In doing so, we provide a link between fungal community ecology and modern coexistence theory (MCT). We first show how community processes and predictions made by MCT can be used to define meaningful scales in fungal ecology. This leads to the novel concept of the unit of community interactions (UCI), a promising conceptual tool for applying MCT to communities of modular organisms with indeterminate clonal growth and hierarchical individuality. We outline plausible coexistence mechanisms structuring fungal communities, and show at what spatial scales and in what habitats they are most likely to act. We end by describing challenges and opportunities for empirical and theoretical research in fungal competitive coexistence.
Collapse
Affiliation(s)
- Miloš Bielčik
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research (ZALF), Eberswalder Str.84, Müncheberg, 15374, Germany
| | - Ulrike E Schlägel
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
| | - Merlin Schäfer
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
- Federal Agency for Nature Conservation, Alte Messe 6, Leipzig, 04103, Germany
| | - Carlos A Aguilar-Trigueros
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Building R2, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Seminaarinkatu 15, Jyväskylä, 40014, Finland
| | - Milica Lakovic
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
| | - Moisés A Sosa-Hernández
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
| | - Edith C Hammer
- Department of Biology, Microbial Ecology, Lund University, Ekologihuset, Sölvegatan 37, Lund, 22362, Sweden
| | - Florian Jeltsch
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
| |
Collapse
|
5
|
Harder CB, Miyauchi S, Virágh M, Kuo A, Thoen E, Andreopoulos B, Lu D, Skrede I, Drula E, Henrissat B, Morin E, Kohler A, Barry K, LaButti K, Salamov A, Lipzen A, Merényi Z, Hegedüs B, Baldrian P, Stursova M, Weitz H, Taylor A, Koriabine M, Savage E, Grigoriev IV, Nagy LG, Martin F, Kauserud H. Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations. CELL GENOMICS 2024; 4:100586. [PMID: 38942024 PMCID: PMC11293592 DOI: 10.1016/j.xgen.2024.100586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/28/2024] [Accepted: 05/28/2024] [Indexed: 06/30/2024]
Abstract
Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.
Collapse
Affiliation(s)
- Christoffer Bugge Harder
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway; Department of Biology, Microbial Ecology Group, Biology Department, Lund University, Lund, Sweden; University of Copenhagen, Department of Biology, Section of Terrestrial Ecology, 2100 Copenhagen Ø, Denmark.
| | - Shingo Miyauchi
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France
| | - Máté Virágh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ella Thoen
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
| | - Bill Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dabao Lu
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
| | - Inger Skrede
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, 163 avenue de Luminy, 13288 Marseille, France; INRAE, UMR 1163, Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, 163 avenue de Luminy, 13288 Marseille, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Asaf Salamov
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Botond Hegedüs
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Martina Stursova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Hedda Weitz
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Andy Taylor
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK; The James Hutton Institute, Aberdeen, UK
| | - Maxim Koriabine
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily Savage
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Francis Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France.
| | - Håvard Kauserud
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
| |
Collapse
|
6
|
Jin XH, Wang YC, Li D, Li Y, He HY, Zhang HB. Diverse Mycena Fungi and Their Potential for Gastrodia elata Germination. J Microbiol Biotechnol 2024; 34:1249-1259. [PMID: 38938004 PMCID: PMC11239410 DOI: 10.4014/jmb.2401.01009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/29/2024]
Abstract
It remains to be determined whether there is a geographical distribution pattern and phylogenetic signals for the Mycena strains with seed germination of the orchid plant Gastrodia elata. This study analyzed the community composition and phylogenetics of 72 Mycena strains associated with G. elata varieties (G. elata. f. glauca and G. elata. f. viridis) using multiple gene fragments (ITS+nLSU+SSU). We found that (1) these diverse Mycena phylogenetically belong to the Basidiospore amyloid group. (2) There is a phylogenetic signal of Mycena for germination of G. elata. Those strains phylogenetically close to M. abramsii, M. polygramma, and an unclassified Mycena had significantly higher germination rates than those to M. citrinomarginata. (3) The Mycena distribution depends on geographic site and G. elata variety. Both unclassified Mycena group 1 and the M. abramsii group were dominant for the two varieties of G. elata; in contrast, the M. citrinomarginata group was dominant in G. elata f. glauca but absent in G. elata f. viridis. Our results indicate that the community composition of numerous Mycena resources in the Zhaotong area varies by geographical location and G. elata variety. Importantly, our results also indicate that Mycena's phylogenetic status is correlated with its germination rate.
Collapse
Affiliation(s)
- Xiao-Han Jin
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan, Kunming, P.R. China
- School of Ecology and Environmental Science, Yunnan University, Kunming, P.R. China
| | - Yu-Chuan Wang
- Gastrodia Tuber Research Institute of Zhaotong, P.R. China
| | - Dong Li
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan, Kunming, P.R. China
- School of Ecology and Environmental Science, Yunnan University, Kunming, P.R. China
| | - Yu Li
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan, Kunming, P.R. China
| | - Hai-Yan He
- The Agriculture and Life Sciences College, Zhaotong University, Zhaotong, P.R. China
- Yunnan Key Laboratory of Gastrodia elata and Fungus Symbiotic Biology, Zhaotong, P.R. China
| | - Han-Bo Zhang
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan, Kunming, P.R. China
| |
Collapse
|
7
|
Daraz U, Erhunmwunse AS, Dubeux JCB, Mackowiak C, Liao HL, Wang XB. Soil fungal community structure and function response to rhizoma perennial peanut cultivars. BMC PLANT BIOLOGY 2024; 24:582. [PMID: 38898415 PMCID: PMC11186081 DOI: 10.1186/s12870-024-05209-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Crop-associated microorganisms play a crucial role in soil nutrient cycling, and crop growth, and health. Fine-scale patterns in soil microbial community diversity and composition are commonly regulated by plant species or genotype. Despite extensive reports in different crop or its cultivar effects on the microbial community, it is uncertain how rhizoma peanut (RP, Arachis glabrata Benth.), a perennial warm-season legume forage that is well-adapted in the southern USA, affects soil microbial community across different cultivars. RESULTS This study explored the influence of seven different RP cultivars on the taxonomic composition, diversity, and functional groups of soil fungal communities through a field trial in Marianna, Florida, Southern USA, using next-generation sequencing technique. Our results showed that the taxonomic diversity and composition of the fungal community differed significantly across RP cultivars. Alpha diversity (Shannon, Simpson, and Pielou's evenness) was significantly higher in Ecoturf but lower in UF_Peace and Florigraze compared to other cultivars (p < 0.001). Phylogenetic diversity (Faith's PD) was lowest in Latitude compared to other cultivars (p < 0.0001). The dominant phyla were Ascomycota (13.34%), Mortierellomycota (3.82%), and Basidiomycota (2.99%), which were significantly greater in Florigraze, UF_Peace, and Ecoturf, respectively. The relative abundance of Neocosmospora was markedly high (21.45%) in UF_Tito and showed large variations across cultivars. The relative abundance of the dominant genera was significantly greater in Arbrook than in other cultivars. There were also significant differences in the co-occurrence network, showing different keystone taxa and more positive correlations than the negative correlations across cultivars. FUNGuild analysis showed that the relative abundance of functional guilds including pathogenic, saprotrophic, endophytic, mycorrhizal and parasitic fungi significantly differed among cultivars. Ecoturf had the greatest relative abundance of mycorrhizal fungal group (5.10 ± 0.44), whereas UF_Peace had the greatest relative abundance of endophytic (4.52 ± 0.56) and parasitic fungi (1.67 ± 0.30) compared to other cultivars. CONCLUSIONS Our findings provide evidence of crop cultivar's effect in shaping fine-scale fungal community patterns in legume-based forage systems.
Collapse
Affiliation(s)
- Umar Daraz
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
| | | | - José C B Dubeux
- North Florida Research and Education Center, University of Florida, Marianna, FL, USA
| | - Cheryl Mackowiak
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Xiao-Bo Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China.
| |
Collapse
|
8
|
Jing L, Shi T, Chang Y, Meng X, He S, Xu H, Yang S, Liu J. Cellulose-based materials in environmental protection: A scientometric and visual analysis review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172576. [PMID: 38649055 DOI: 10.1016/j.scitotenv.2024.172576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
As sustainable materials, cellulose-based materials have attracted significant attention in the field of environmental protection, resulting in the publication of numerous academic papers. However, there is a scarcity of literature that involving scientometric analysis within this specific domain. This review aims to address this gap and highlight recent research in this field by utilizing scientometric analysis and a historical review. As a result, 21 highly cited articles and 10 mostly productive journals were selected out. The scientometric analysis reveals that recent studies were objectively clustered into five interconnected main themes: extraction of cellulose from raw materials and its degradation, adsorption of pollutants using cellulose-based materials, cellulose-acetate-based membrane materials, nanocellulose-based materials, and other cellulose-based materials such as carboxymethyl cellulose and bacterial cellulose for environmental protection. Analyzing the distribution of author keywords and thoroughly examining relevant literature, the research focuses within these five themes were summarized. In the future, the development of eco-friendly and cost-effective methods for extracting and preparing cellulose and its derivatives, particularly nanocellulose-based materials, remains an enduring pursuit. Additionally, machine learning techniques holds promise for the advancement and application of cellulose-based materials. Furthermore, there is potential to expand the research and application scope of cellulose-based materials for environmental protection.
Collapse
Affiliation(s)
- Liandong Jing
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Institute of Qinghai-Tibet Plateau, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Tianyu Shi
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Institute of Qinghai-Tibet Plateau, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Yulung Chang
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Xingliang Meng
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Shuai He
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Institute of Qinghai-Tibet Plateau, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Hang Xu
- School of Material Science & Chemical Engineering, Harbin University of Science and Technology, Harbin, China
| | - Shengtao Yang
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Institute of Qinghai-Tibet Plateau, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Jia Liu
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Institute of Qinghai-Tibet Plateau, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China.
| |
Collapse
|
9
|
Prieto-Fernández F, Lambert S, Kujala K. Assessment of microbial communities from cold mine environments and subsequent enrichment, isolation and characterization of putative antimony- or copper-metabolizing microorganisms. Front Microbiol 2024; 15:1386120. [PMID: 38855773 PMCID: PMC11160943 DOI: 10.3389/fmicb.2024.1386120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/23/2024] [Indexed: 06/11/2024] Open
Abstract
Mining activities, even in arctic regions, create waste materials releasing metals and metalloids, which have an impact on the microorganisms inhabiting their surroundings. Some species can persist in these areas through tolerance to meta(loid)s via, e.g., metabolic transformations. Due to the interaction between microorganisms and meta(loid)s, interest in the investigation of microbial communities and their possible applications (like bioremediation or biomining) has increased. The main goal of the present study was to identify, isolate, and characterize microorganisms, from subarctic mine sites, tolerant to the metalloid antimony (Sb) and the metal copper (Cu). During both summer and winter, samples were collected from Finnish mine sites (site A and B, tailings, and site C, a water-treatment peatland) and environmental parameters were assessed. Microorganisms tolerant to Sb and Cu were successfully enriched under low temperatures (4°C), creating conditions that promoted the growth of aerobic and fermenting metal(loid) tolerating or anaerobic metal(loid) respiring organism. Microbial communities from the environment and Sb/Cu-enriched microorganisms were studied via 16S rRNA amplicon sequencing. Site C had the highest number of taxa and for all sites, an expected loss of biodiversity occurred when enriching the samples, with genera like Prauserella, Pseudomonas or Clostridium increasing their relative abundances and others like Corynebacterium or Kocuria reducing in relative abundance. From enrichments, 65 putative Sb- and Cu-metabolizing microorganisms were isolated, showing growth at 0.1 mM to 10 mM concentrations and 0°C to 40°C temperatures. 16S rRNA gene sequencing of the isolates indicated that most of the putative anaerobically Sb-respiring tolerators were related to the genus Clostridium. This study represents the first isolation, to our knowledge, of putative Sb-metabolizing cold-tolerant microorganisms and contributes to the understanding of metal (loid)-tolerant microbial communities in Arctic mine sites.
Collapse
|
10
|
Leifheit EF, Camenzind T, Lehmann A, Andrade-Linares DR, Fussan M, Westhusen S, Wineberger TM, Rillig MC. Fungal traits help to understand the decomposition of simple and complex plant litter. FEMS Microbiol Ecol 2024; 100:fiae033. [PMID: 38486354 PMCID: PMC11022653 DOI: 10.1093/femsec/fiae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 04/18/2024] Open
Abstract
Litter decomposition is a key ecosystem process, relevant for the release and storage of nutrients and carbon in soil. Soil fungi are one of the dominant drivers of organic matter decomposition, but fungal taxa differ substantially in their functional ability to decompose plant litter. Knowledge is mostly based on observational data and subsequent molecular analyses and in vitro studies have been limited to forest ecosystems. In order to better understand functional traits of saprotrophic soil fungi in grassland ecosystems, we isolated 31 fungi from a natural grassland and performed several in vitro studies testing for i) leaf and wood litter decomposition, ii) the ability to use carbon sources of differing complexity, iii) the enzyme repertoire. Decomposition strongly varied among phyla and isolates, with Ascomycota decomposing the most and Mucoromycota decomposing the least. The phylogeny of the fungi and their ability to use complex carbon were the most important predictors for decomposition. Our findings show that it is crucial to understand the role of individual members and functional groups within the microbial community. This is an important way forward to understand the role of microbial community composition for the prediction of litter decomposition and subsequent potential carbon storage in grassland soils.
Collapse
Affiliation(s)
- Eva F Leifheit
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Anika Lehmann
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Diana R Andrade-Linares
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Research Unit for Comparative Microbiome Analyses – COMI, 85764 Neuherberg, Germany
| | - Max Fussan
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Sophia Westhusen
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
| | - Till M Wineberger
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| |
Collapse
|
11
|
Yuan H, Li L, Wang Y, Lin S. Succession of diversity, assembly mechanisms, and activities of the microeukaryotic community throughout Scrippsiella acuminata (Dinophyceae) bloom phases. HARMFUL ALGAE 2024; 134:102626. [PMID: 38705614 DOI: 10.1016/j.hal.2024.102626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 04/02/2024] [Accepted: 04/06/2024] [Indexed: 05/07/2024]
Abstract
Harmful algal bloom (HAB) is a rapidly expanding marine ecological hazard. Although numerous studies have been carried out about the ecological impact and the ecological mechanism of HAB outbreaks, few studies have comprehensively addressed the shifts of species composition, metabolic activity level, driving factors and community assembly mechanisms of microeukaryotic plankton in the course of the bloom event. To fill the gap of research, we conducted 18S ribosomal DNA and RNA sequencing during the initiation, development, sustenance and decline stages of a Scrippsiella acuminata (S. acuminata) bloom at the coastal sea of Fujian Province, China. We found that the bloom event caused a decrease in microeukaryotic plankton species diversity and increase in community homogeneity. Our results revealed that the RNA- and DNA-inferred communities were similar, but α-diversity was more dynamic in RNA- than in DNA-inferred communities. The main taxa with high projected metabolic activity (with RNA:DNA ratio as the proxy) during the bloom included dinoflagellates, Cercozoa, Chlorophyta, Protalveolata, and diatoms. The role of deterministic processes in microeukaryotic plankton community assembly increased during the bloom, but stochastic processes were always the dominant assembly mechanism throughout the bloom process. Our findings improve the understanding of temporal patterns, driving factors and assembly mechanisms underlying the microeukarytic plankton community in a dinoflagellate bloom.
Collapse
Affiliation(s)
- Huatao Yuan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, and Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361102, China; College of Fisheries, Observation and Research Station on Water Ecosystem in Danjiangkou Reservoir of Henan Province, Henan Normal University, Xinxiang 453007, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, and Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361102, China
| | - Yujie Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, and Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361102, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, and Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361102, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao 266000, Shandong, China; Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
| |
Collapse
|
12
|
Khatri-Chhetri U, Banerjee S, Thompson KA, Quideau SA, Boyce MS, Bork EW, Carlyle CN. Cattle grazing management affects soil microbial diversity and community network complexity in the Northern Great Plains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169353. [PMID: 38104847 DOI: 10.1016/j.scitotenv.2023.169353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Soil microbial communities play a vital role in the biogeochemical cycling and ecological functioning of grassland, but may be affected by common land uses such as cattle grazing. Changes in microbial diversity and network complexity can affect key ecosystem functions such as nutrient cycling. However, it is not well known how microbial diversity and network complexity respond to grazing in the Northern Great Plains. Consequently, it is important to understand whether variation in grazing management alters the diversity and complexity of grassland microbial communities. We compared the effect of intensive adaptive multi-paddock (AMP) grazing and conventional grazing practices on soil microbial communities using 16S/ITS amplicon sequencing. Samples were collected from grasslands in 13 AMP ranches and 13 neighboring, conventional ranches located across the Canadian prairies. We found that AMP grazing increased fungal diversity and evenness, and led to more complex microbial associations. Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes were keystone taxa associated with AMP grazing, while Actinobacteria, Acidobacteria, Proteobacteria, and Armatimonadetes were keystone taxa under conventional grazing. Besides overall grazing treatment effects, specific grazing metrics like cattle stocking rate and rest-to-grazing ratio affected microbial richness and diversity. Bacterial and fungal richness increased with elevated stocking rate, and fungal richness and diversity increased directly with the rest-to-grazing ratio. These results suggest that AMP grazing may improve ecosystem by enhancing fungal diversity and increasing microbial network complexity and connectivity.
Collapse
Affiliation(s)
- Upama Khatri-Chhetri
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada.
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Karen A Thompson
- Trent School of Environment, Trent University, Peterborough, ON K9L 0G2, Canada
| | - Sylvie A Quideau
- Department of Renewable Resources, Earth Science Building University of Alberta, Edmonton, AB T6G 2E3, Canada
| | - Mark S Boyce
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Edward W Bork
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Cameron N Carlyle
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| |
Collapse
|
13
|
Gacura MD, Zak DR, Blackwood CB. From individual leaves to forest stands: importance of niche, distance decay, and stochasticity vary by ecosystem type and functional group for fungal community composition. FEMS Microbiol Ecol 2024; 100:fiae016. [PMID: 38373845 PMCID: PMC10913062 DOI: 10.1093/femsec/fiae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/26/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024] Open
Abstract
Community assembly is influenced by environmental niche processes as well as stochastic processes that can be spatially dependent (e.g. dispersal limitation) or independent (e.g. priority effects). Here, we sampled senesced tree leaves as unit habitats to investigate fungal community assembly at two spatial scales: (i) small neighborhoods of overlapping leaves from differing tree species and (ii) forest stands of differing ecosystem types. Among forest stands, ecosystem type explained the most variation in community composition. Among adjacent leaves within stands, variability in fungal composition was surprisingly high. Leaf type was more important in stands with high soil fertility and dominated by differing tree mycorrhizal types (sugar maple vs. basswood or red oak), whereas distance decay was more important in oak-dominated forest stands with low soil fertility. Abundance of functional groups was explained by environmental factors, but predictors of taxonomic composition within differing functional groups were highly variable. These results suggest that fungal community assembly processes are clearest for functional group abundances and large spatial scales. Understanding fungal community assembly at smaller spatial scales will benefit from further study focusing on differences in drivers for different ecosystems and functional groups, as well as the importance of spatially independent factors such as priority effects.
Collapse
Affiliation(s)
- Matthew D Gacura
- Department of Biological Sciences, Kent State University, 800 E. Summit St., Kent, OH 44242, United States
- Biology Department, Gannon University, 109 University Square, Erie, PA 16541, United States
| | - Donald R Zak
- School for Environment and Sustainability, University of Michigan, 440 Church St., Ann Arbor, MI 48109, United States
| | - Christopher B Blackwood
- Department of Biological Sciences, Kent State University, 800 E. Summit St., Kent, OH 44242, United States
- Department of Plant, Soil, and Microbial Sciences and Department of Plant Biology, Michigan State University, 1066 Bogue St., East Lansing, MI 48842, United States
| |
Collapse
|
14
|
Bautista-Cruz A, Aquino-Bolaños T, Hernández-Canseco J, Quiñones-Aguilar EE. Cellulolytic Aerobic Bacteria Isolated from Agricultural and Forest Soils: An Overview. BIOLOGY 2024; 13:102. [PMID: 38392320 PMCID: PMC10886624 DOI: 10.3390/biology13020102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
This review provides insights into cellulolytic bacteria present in global forest and agricultural soils over a period of 11 years. It delves into the study of soil-dwelling cellulolytic bacteria and the enzymes they produce, cellulases, which are crucial in both soil formation and the carbon cycle. Forests and agricultural activities are significant contributors to the production of lignocellulosic biomass. Forest ecosystems, which are key carbon sinks, contain 20-30% cellulose in their leaf litter. Concurrently, the agricultural sector generates approximately 998 million tons of lignocellulosic waste annually. Predominant genera include Bacillus, Pseudomonas, Stenotrophomonas, and Streptomyces in forests and Bacillus, Streptomyces, Pseudomonas, and Arthrobacter in agricultural soils. Selection of cellulolytic bacteria is based on their hydrolysis ability, using artificial cellulose media and dyes like Congo red or iodine for detection. Some studies also measure cellulolytic activity in vitro. Notably, bacterial cellulose hydrolysis capability may not align with their cellulolytic enzyme production. Enzymes such as GH1, GH3, GH5, GH6, GH8, GH9, GH10, GH12, GH26, GH44, GH45, GH48, GH51, GH74, GH124, and GH148 are crucial, particularly GH48 for crystalline cellulose degradation. Conversely, bacteria with GH5 and GH9 often fail to degrade crystalline cellulose. Accurate identification of cellulolytic bacteria necessitates comprehensive genomic analysis, supplemented by additional proteomic and transcriptomic techniques. Cellulases, known for degrading cellulose, are also significant in healthcare, food, textiles, bio-washing, bleaching, paper production, ink removal, and biotechnology, emphasizing the importance of discovering novel cellulolytic strains in soil.
Collapse
Affiliation(s)
- Angélica Bautista-Cruz
- Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Teodulfo Aquino-Bolaños
- Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Jessie Hernández-Canseco
- Doctoral Programme in Conservation and Use of Natural Resources, Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Evangelina Esmeralda Quiñones-Aguilar
- Laboratorio de Fitopatología de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Camino Arenero 1227, El Bajío del Arenal, Zapopan 45019, Jalisco, Mexico
| |
Collapse
|
15
|
Jaeger ACH, Hartmann M, Conz RF, Six J, Solly EF. Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13211. [PMID: 37991154 PMCID: PMC10866073 DOI: 10.1111/1758-2229.13211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.
Collapse
Affiliation(s)
- Astrid C. H. Jaeger
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Martin Hartmann
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Rafaela Feola Conz
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Johan Six
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Emily F. Solly
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
- Helmholtz Centre for Environmental Research—UFZLeipzigGermany
| |
Collapse
|
16
|
Datta R. Enzymatic degradation of cellulose in soil: A review. Heliyon 2024; 10:e24022. [PMID: 38234915 PMCID: PMC10792583 DOI: 10.1016/j.heliyon.2024.e24022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/13/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024] Open
Abstract
Cellulose degradation is a critical process in soil ecosystems, playing a vital role in nutrient cycling and organic matter decomposition. Enzymatic degradation of cellulosic biomass is the most sustainable and green method of producing liquid biofuel. It has gained intensive research interest with future perspective as the majority of terrestrial lignocellulose biomass has a great potential to be used as a source of bioenergy. However, the recalcitrant nature of lignocellulose limits its use as a source of energy. Noteworthy enough, enzymatic conversion of cellulose biomass could be a leading future technology. Fungal enzymes play a central role in cellulose degradation. Our understanding of fungal cellulases has substantially redirected in the past few years with the discovery of a new class of enzymes and Cellulosome. Efforts have been made from time to time to develop an economically viable method of cellulose degradation. This review provides insights into the current state of knowledge regarding cellulose degradation in soil and identifies areas where further research is needed.
Collapse
Affiliation(s)
- Rahul Datta
- Department of Geology and Pedology, Faculty of Forestry and Wood Technology. Mendel University In Brno, Czech Republic
| |
Collapse
|
17
|
Sebastián M, Giner CR, Balagué V, Gómez-Letona M, Massana R, Logares R, Duarte CM, Gasol JM. The active free-living bathypelagic microbiome is largely dominated by rare surface taxa. ISME COMMUNICATIONS 2024; 4:ycae015. [PMID: 38456147 PMCID: PMC10919342 DOI: 10.1093/ismeco/ycae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 03/09/2024]
Abstract
A persistent microbial seed bank is postulated to sustain the marine biosphere, and recent findings show that prokaryotic taxa present in the ocean's surface dominate prokaryotic communities throughout the water column. Yet, environmental conditions exert a tight control on the activity of prokaryotes, and drastic changes in these conditions are known to occur from the surface to deep waters. The simultaneous characterization of the total (DNA) and active (i.e. with potential for protein synthesis, RNA) free-living communities in 13 stations distributed across the tropical and subtropical global ocean allowed us to assess their change in structure and diversity along the water column. We observed that active communities were surprisingly more similar along the vertical gradient than total communities. Looking at the vertical connectivity of the active vs. the total communities, we found that taxa detected in the surface sometimes accounted for more than 75% of the active microbiome of bathypelagic waters (50% on average). These active taxa were generally rare in the surface, representing a small fraction of all the surface taxa. Our findings show that the drastic vertical change in environmental conditions leads to the inactivation and disappearance of a large proportion of surface taxa, but some surface-rare taxa remain active (or with potential for protein synthesis) and dominate the bathypelagic active microbiome.
Collapse
Affiliation(s)
- Marta Sebastián
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Caterina R Giner
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Vanessa Balagué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Markel Gómez-Letona
- Instituto de Oceanografía y Cambio Global, Universidad de Las Palmas de Gran Canaria, Parque Científico Tecnológico Marino de Taliarte, s/n, Telde, Las Palmas 35214, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Carlos M Duarte
- Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| |
Collapse
|
18
|
Hao Z, Wang Q, Wang J, Deng Y, Yan Z, Tian L, Jiang H. Water Level Fluctuations Modulate the Microbiomes Involved in Biogeochemical Cycling in Floodplains. MICROBIAL ECOLOGY 2023; 87:24. [PMID: 38159125 DOI: 10.1007/s00248-023-02331-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
Drastic changes in hydrological conditions within floodplain ecosystems create distinct microbial habitats. However, there remains a lack of exploration regarding the variations in microbial function potentials across the flooding and drought seasons. In this study, metagenomics and environmental analyses were employed in floodplains that experience hydrological variations across four seasons. Analysis of functional gene composition, encompassing nitrogen, carbon, and sulfur metabolisms, revealed apparent differences between the flooding and drought seasons. The primary environmental drivers identified were water level, overlying water depth, submergence time, and temperature. Specific modules, e.g., the hydrolysis of β-1,4-glucosidic bond, denitrification, and dissimilatory/assimilatory nitrate reduction to ammonium, exhibited higher relative abundance in summer compared to winter. It is suggested that cellulose degradation was potentially coupled with nitrate reduction during the flooding season. Phylogenomic analysis of metagenome-assembled genomes (MAGs) unveiled that the Desulfobacterota lineage possessed abundant nitrogen metabolism genes supported by pathway reconstruction. Variation of relative abundance implied its environmental adaptability to both the wet and dry seasons. Furthermore, a novel order was found within Methylomirabilota, containing nitrogen reduction genes in the MAG. Overall, this study highlights the crucial role of hydrological factors in modulating microbial functional diversity and generating genomes with abundant nitrogen metabolism potentials.
Collapse
Affiliation(s)
- Zheng Hao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qianhong Wang
- Changjiang Nanjing Waterway Engineering Bureau, Nanjing, 210011, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Zaisheng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Linqi Tian
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China.
| |
Collapse
|
19
|
Wang H, Xu Y, Kumar A, Knorr KH, Zhao X, Perez JPH, Sun G, Yu ZG. Temperature and organic carbon quality control the anaerobic carbon mineralization in peat profiles via modulating microbes: A case study of Changbai Mountain. ENVIRONMENTAL RESEARCH 2023; 237:116904. [PMID: 37595828 DOI: 10.1016/j.envres.2023.116904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/01/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Peatlands account for a significant fraction of the global carbon stock. However, the complex interplay of abiotic and biotic factors governing anaerobic carbon mineralization in response to warming remains unclear. In this study, peat sediments were collected from a typical northern peatland-Changbai Mountain to investigate the behavior and mechanism of anaerobic carbon mineralization in response to depth (0-200 cm) and temperature (5 °C, 15 °C and 20 °C), by integrating geochemical and microbial analysis. Several indices including humification indexes (HI), aromaticity, and water extractable organic carbon (WEOC) components were applied to evaluate carbon quality, while 16S rRNA sequencing was used to measure microbial composition. Regardless of temperature, degradations of carbon quality and associated reduction in microbial abundance as well as diversity resulted in a decrease in anaerobic carbon mineralization (both CO2 and CH4) towards greater depth. Warming either from 5 °C to 15 °C or 20 °C significantly increased anaerobic carbon mineralization in all depth profiles by improving carbon availability. Enhanced carbon availabilities were mediated by the change in microbial composition (p < 0.01) and an increase in metabolic activities, which was particularly evident in the enhanced β-glucosidase activity and microbial collaborations. A remarkable increase of over 10-fold in the relative abundance of the Geothrix genus was observed under warming. Overall, warming resulted in an enhanced contribution of CH4 emission and a higher ratio of hydrogenotrophic methanogenesis, as evidenced by carbon isotope fractionation factors. In addition, deep peat soils (>100 cm) with recalcitrant carbon demonstrated greater temperature sensitivity (Q10: ∼2.0) than shallow peat soils (Q10:∼1.2) when temperature increased from 15 °C to 20 °C. The findings of this study have significantly deepened our understanding for mechanisms of carbon quality and microbe-driven anaerobic carbon mineralization in peatlands under global warming.
Collapse
Affiliation(s)
- Hongyan Wang
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, 210044, China; Key Laboratory of Watershed Earth Surface Processes and Ecological Security, Zhejiang Normal University, Jinhua, 321004, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yijie Xu
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Amit Kumar
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Klaus-Holger Knorr
- University of Münster, Institute for Landscape Ecology, Ecohydrology and Biogeochemistry Group, Heisenbergstr. 2, Münster, 48149, Germany
| | - Xiaoning Zhao
- School of Geographical Sciences, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jeffrey Paulo H Perez
- Sec. 3.2 Organic Geochemistry, GFZ German Research Centre for Geosciences, Telegrafenberg, 14473, Potsdam, Germany
| | - Guoxin Sun
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Zhi-Guo Yu
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| |
Collapse
|
20
|
Dash PK, Bhattacharyya P, Shahid M, Kumar U, Padhy SR, Swain CK, Senapati A, Bihari P, Nayak AK. Impact of long-term resource conservation techniques on biogeochemical characteristics and biological soil quality indicators in a rice green-gram farming system. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:7979-7997. [PMID: 37515727 DOI: 10.1007/s10653-023-01713-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/20/2023] [Indexed: 07/31/2023]
Abstract
Nutrient management in resource conservation practices influence the structural and functional microbial diversities and thereby affect biological processes and biochemical properties in soil. We studied the long-term effects of resource conservation technologies on functional microbial diversity and their interactions with soil biochemical properties and enzymatic activities in tropical rice-green gram cropping system. The experiment includes seven treatments viz., conventional practice (CC), brown manuring (BM), green manuring (GM), wet direct drum sowing, zero tillage, green manuring-customized leaf colour chart based-N application (GM-CLCC-N) and biochar (BC) application. The result of the present study revealed that microbial biomass nitrogen (N), carbon (C) and phosphorus (P) in GM practice were increased by 23.3, 37.7 and 35.1%, respectively than CC. GM, BM and GM-CLCC-N treatments provide higher yields than conventional practice. The average well color development value, Shannon index and McIntosh index were significantly higher by 26.6%, 86.9% and 29.2% in GM as compared to control treatment. So, from this study we can conclude that resource conservation practices like GM, GM-CLCC N and BM in combination with chemical fertilizers provide easily decomposable carbon source to support the microbial growth. Moreover, dominance of microbial activity in biomass amended treatments (GM, GM-CLCC N and BM) indicated that these treatments could supply good amount of labile C sources on real time basis for microbial growth that may protect the stable C fraction in soil, hence could support higher yield and soil organic carbon build-up in long run under rice-green gram soil.
Collapse
Affiliation(s)
- P K Dash
- Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006, India.
| | - P Bhattacharyya
- Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006, India
| | - Mohammad Shahid
- Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006, India
| | - U Kumar
- Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006, India
| | - S R Padhy
- Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006, India
| | - C K Swain
- Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006, India
| | - A Senapati
- Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006, India
| | - P Bihari
- Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006, India
| | - A K Nayak
- Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006, India.
| |
Collapse
|
21
|
Zerouki C, Chakraborty K, Kuittinen S, Pappinen A, Turunen O. Whole-genome sequence and mass spectrometry study of the snow blight fungus Phacidium infestans (Karsten) DSM 5139 growing at freezing temperatures. Mol Genet Genomics 2023; 298:1449-1466. [PMID: 37815644 PMCID: PMC10657286 DOI: 10.1007/s00438-023-02073-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023]
Abstract
Phacidium infestans (synonym Gremmenia infestans) is a significant pathogen that impacts Pinus species across the northern regions of Europe and Asia. This study introduces the genome sequence of P. infestans Karsten DSM 5139 (Phain), obtained through Pacbio technology. The assembly resulted in 44 contigs, with a total genome size of 36,805,277 bp and a Guanine-Cytosine content of 46.4%. Genome-mining revealed numerous putative biosynthetic gene clusters that code for virulence factors and fungal toxins. The presence of the enzyme pisatin demethylase was indicative of the potential of Phain to detoxify its environment from the terpenoid phytoalexins produced by its host as a defense mechanism. Proteomic analysis revealed the potential survival strategies of Phain under the snow, which included the production of antifreeze proteins, trehalose synthesis enzymes, desaturases, proteins related to elongation of very long-chain fatty acids, and stress protein responses. Study of protein GH11 endoxylanase expressed in Escherichia coli showed an acidic optimum pH (pH 5.0) and a low optimum temperature (45 °C), which is reflective of the living conditions of the fungus. Mass spectrometry analysis of the methanol extract of Phain, incubated at - 3 °C and 22 °C, revealed differences in the produced metabolites. Both genomic and mass spectrometry analyses showed the ability of Phain to adapt its metabolic processes and secretome to freezing temperatures through the production of osmoprotectant and cryoprotectant metabolites. This comprehensive exploration of Phain's genome sequence, proteome, and secretome not only advances our understanding of its unique adaptive mechanisms but also expands the possibilities of biotechnological applications.
Collapse
Affiliation(s)
- C Zerouki
- School of Forest Sciences, University of Eastern Finland, Yliopistokatu 7, 80101, Joensuu, Finland.
| | - K Chakraborty
- School of Forest Sciences, University of Eastern Finland, Yliopistokatu 7, 80101, Joensuu, Finland
| | - S Kuittinen
- School of Forest Sciences, University of Eastern Finland, Yliopistokatu 7, 80101, Joensuu, Finland
| | - A Pappinen
- School of Forest Sciences, University of Eastern Finland, Yliopistokatu 7, 80101, Joensuu, Finland
| | - O Turunen
- School of Forest Sciences, University of Eastern Finland, Yliopistokatu 7, 80101, Joensuu, Finland
| |
Collapse
|
22
|
Cheng G, Zhang X, Zhu M, Zhang Z, Jing L, Wang L, Li Q, Zhang X, Wang H, Wang W. Tree diversity, growth status, and spatial distribution affected soil N availability and N 2O efflux: Interaction with soil physiochemical properties. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118375. [PMID: 37356331 DOI: 10.1016/j.jenvman.2023.118375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 06/04/2023] [Accepted: 06/10/2023] [Indexed: 06/27/2023]
Abstract
Soil nitrogen (N) is an essential nutrient for tree growth, and excessive N is a source of pollution. This paper aims to define the effects of plant diversity and forest structure on various aspects of soil N cycling. Herein, we collected soils from 720 plots to measure total N content (TN), alkali-hydrolyzed N (AN), nitrate N (NO3--N), ammonium N (NH4+-N) in a 7.2 ha experimental forest in northeast China. Four plant diversity indices, seven structural metrics, four soil properties, and in situ N2O efflux were also measured. We found that: 1) high tree diversity had 1.3-1.4-fold NO3--N, 1.1-fold NH4+-N, and 1.5-1.8-fold N2O efflux (p < 0.05). 2) Tree growth decreased soil TN, AN, and NO3--N by more than 13%, and tree mixing and un-uniform distribution increased TN, AN, and NH4+-N by 11-22%. 3) Soil organic carbon (SOC) explained 34.3% of the N variations, followed by soil water content (1.5%), tree diameter (1.5%) and pH (1%), and soil bulk density (0.5%). SOC had the most robust linear relations to TN (R2 = 0.59) and AN (R2 = 0.5). 4) The partial least squares path model revealed that the tree diversity directly increased NO3--N, NH4+-N, and N2O efflux, and they were strengthened indirectly from soil properties by 1%-4%. The effects of tree size-density (-0.24) and spatial structure (0.16) were mainly achieved via their soil interaction and thus indirectly decreased NH4+-N, AN, and TN. Overall, high tree diversity forests improved soil N availability and N2O efflux, and un-uniform spatial tree assemblages could partially balance the soil N consumed by tree growth. Our data support soil N management in high northern hemisphere temperate forests from tree diversity and forest structural regulations.
Collapse
Affiliation(s)
- Guanchao Cheng
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Xu Zhang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Meina Zhu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Zhonghua Zhang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Lixin Jing
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Lei Wang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Qi Li
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Xiting Zhang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Huimei Wang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
| | - Wenjie Wang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China; Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, CAS, Changchun, 130102, China.
| |
Collapse
|
23
|
Zeng Q, Lebreton A, Auer L, Man X, Jia L, Wang G, Gong S, Lombard V, Buée M, Wu G, Dai Y, Yang Z, Martin FM. Stable functional structure despite high taxonomic variability across fungal communities in soils of old-growth montane forests. MICROBIOME 2023; 11:217. [PMID: 37779194 PMCID: PMC10544587 DOI: 10.1186/s40168-023-01650-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/11/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Major advances over the past decade in molecular ecology are providing access to soil fungal diversity in forest ecosystems worldwide, but the diverse functions and metabolic capabilities of this microbial community remain largely elusive. We conducted a field survey in montane old-growth broadleaved and conifer forests, to investigate the relationship between soil fungal diversity and functional genetic traits. To assess the extent to which variation in community composition was associated with dominant tree species (oak, spruce, and fir) and environmental variations in the old-growth forests in the Jade Dragon Snow Mountain in Yunnan Province, we applied rDNA metabarcoding. We also assessed fungal gene expression in soil using mRNA sequencing and specifically assessed the expression of genes related to organic matter decomposition and nutrient acquisition in ectomycorrhizal and saprotrophic fungi. RESULTS Our taxonomic profiling revealed striking shifts in the composition of the saprotrophic and ectomycorrhizal guilds among the oak-, fir-, and spruce-dominated forests. The core fungal microbiome comprised only ~ 20% of the total OTUs across all soil samples, although the overlap between conifer-associated communities was substantial. In contrast, seasonality and soil layer explained only a small proportion of the variation in community structure. However, despite their highly variable taxonomic composition, fungal guilds exhibited remarkably similar functional traits for growth-related and core metabolic pathways across forest associations, suggesting ecological redundancy. However, we found that the expression profiles of genes related to polysaccharide and protein degradation and nutrient transport notably varied between and within the fungal guilds, suggesting niche adaptation. CONCLUSIONS Overall, our metatranscriptomic analyses revealed the functional potential of soil fungal communities in montane old-growth forests, including a suite of specialized genes and taxa involved in organic matter decomposition. By linking genes to ecological traits, this study provides insights into fungal adaptation strategies to biotic and environmental factors, and sheds light on the importance of understanding functional gene expression patterns in predicting ecosystem functioning. Video Abstract.
Collapse
Affiliation(s)
- Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, Beijing, 100083, China
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
- INRAE, Aix-Marseille Université, Biodiversité et Biotechnologie Fongiques, 13009, Marseille, France
| | - Lucas Auer
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
| | - Xiaowu Man
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Liukun Jia
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Gengshen Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, 650201, Yunnan, China
| | - Sai Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Vincent Lombard
- Architecture Et Fonction Des Macromolécules Biologiques, CNRS, Aix-Marseille Université, UMR 7257, 13288, Marseille, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
| | - Gang Wu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, 650201, Yunnan, China
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, Beijing, 100083, China.
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Zhuliang Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, 650201, Yunnan, China.
| | - Francis M Martin
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, Beijing, 100083, China.
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France.
| |
Collapse
|
24
|
Harder CB, Hesling E, Botnen SS, Lorberau KE, Dima B, von Bonsdorff-Salminen T, Niskanen T, Jarvis SG, Ouimette A, Hester A, Hobbie EA, Taylor AFS, Kauserud H. Mycena species can be opportunist-generalist plant root invaders. Environ Microbiol 2023; 25:1875-1893. [PMID: 37188366 DOI: 10.1111/1462-2920.16398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
Traditional strict separation of fungi into ecological niches as mutualist, parasite or saprotroph is increasingly called into question. Sequences of assumed saprotrophs have been amplified from plant root interiors, and several saprotrophic genera can invade and interact with host plants in laboratory growth experiments. However, it is uncertain if root invasion by saprotrophic fungi is a widespread phenomenon and if laboratory interactions mirror field conditions. Here, we focused on the widespread and speciose saprotrophic genus Mycena and performed (1) a systematic survey of their occurrences (in ITS1/ITS2 datasets) in mycorrhizal roots of 10 plant species, and (2) an analysis of natural abundances of 13 C/15 N stable isotope signatures of Mycena basidiocarps from five field locations to examine their trophic status. We found that Mycena was the only saprotrophic genus consistently found in 9 out of 10 plant host roots, with no indication that the host roots were senescent or otherwise vulnerable. Furthermore, Mycena basidiocarps displayed isotopic signatures consistent with published 13 C/15 N profiles of both saprotrophic and mutualistic lifestyles, supporting earlier laboratory-based studies. We argue that Mycena are widespread latent invaders of healthy plant roots and that Mycena species may form a spectrum of interactions besides saprotrophy also in the field.
Collapse
Affiliation(s)
- Christoffer Bugge Harder
- Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Microbial Ecology, Lund University, Lund, Sweden
- Department of Biology, Section of Terrestrial Ecology, University of Copenhagen, Copenhagen, Denmark
| | - Emily Hesling
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Synnøve S Botnen
- Department of Biosciences, University of Oslo, Oslo, Norway
- Oslo Metropolitan University, Oslo, Norway
| | - Kelsey E Lorberau
- Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Arctic and Marine Biology, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Bálint Dima
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
- Botany Unit, Finnish Museum of Natural History LUOMUS, University of Helsinki, Helsinki, Finland
| | | | - Tuula Niskanen
- Botany Unit, Finnish Museum of Natural History LUOMUS, University of Helsinki, Helsinki, Finland
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey, UK
| | | | - Andrew Ouimette
- Earth Systems Research Center, University of New Hampshire, Durham, New Hampshire, USA
| | | | - Erik A Hobbie
- Earth Systems Research Center, University of New Hampshire, Durham, New Hampshire, USA
| | - Andy F S Taylor
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- The James Hutton Institute, Aberdeen, UK
| | | |
Collapse
|
25
|
Wang Y, Zheng G, Zhao Y, Bo H, Li C, Dong J, Wang Y, Yan S, Zhang F, Liu J. Different bacterial and fungal community patterns in restored habitats in coal-mining subsidence areas. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:104304-104318. [PMID: 37700132 DOI: 10.1007/s11356-023-29744-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/03/2023] [Indexed: 09/14/2023]
Abstract
Soil microbiota, which plays a fundamental role in ecosystem functioning, is sensitive to environmental changes. Studying soil microbial ecological patterns can help to understand the consequences of environmental disturbances on soil microbiota and hence ecosystem services. The different habitats with critical environmental gradients generated through the restoration of coal-mining subsidence areas provide an ideal area to explore the response of soil microbiota to environmental changes. Here, based on high-throughput sequencing, we revealed the patterns of soil bacterial and fungal communities in habitats with different land-use types (wetland, farmland, and grassland) and with different restored times which were generated during the ecological restoration of a typical coal-mining subsidence area in Jining City, China. The α-diversity of bacterial was higher in wetland than in farmland and grassland, while that of fungi had no discrepancy among the three habitats. The β-diversity of bacterial community in the grassland was lower than in the farmland, and fungal community was significant different in all three habitats, showing wetland, grassland, and farmland from high to low. The β-diversity of the bacterial community decreased with restoration time while that of the fungal community had no significant change in the longer-restoration-time area. Furthermore, soil electrical conductivity was the most important driver for both bacterial and fungal communities. Based on the taxonomic difference among different habitats, we identified a group of biomarkers for each habitat. The study contributes to understand the microbial patterns during the ecological restoration of coal-mining subsidence areas, which has implications for the efficient ecological restoration of subsidence areas.
Collapse
Affiliation(s)
- Yijing Wang
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Guodong Zheng
- Technology Innovation Center of Restoration and Reclamation in Mining induced Subsidence Land, Ministry of Natural Resources, Shandong Provincial Lunan Geology and Exploration Institute (Shandong Provincial Bureau of Geology and Mineral Resources No.2 Geological Brigade), Jining, 272000, China.
| | - Yongkang Zhao
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Huaizhi Bo
- Technology Innovation Center of Restoration and Reclamation in Mining induced Subsidence Land, Ministry of Natural Resources, Shandong Provincial Lunan Geology and Exploration Institute (Shandong Provincial Bureau of Geology and Mineral Resources No.2 Geological Brigade), Jining, 272000, China
| | - Changchao Li
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Junyu Dong
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Yan Wang
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Shuwan Yan
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Fanglong Zhang
- Technology Innovation Center of Restoration and Reclamation in Mining induced Subsidence Land, Ministry of Natural Resources, Shandong Provincial Lunan Geology and Exploration Institute (Shandong Provincial Bureau of Geology and Mineral Resources No.2 Geological Brigade), Jining, 272000, China
| | - Jian Liu
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| |
Collapse
|
26
|
Behnke-Borowczyk J, Korzeniewicz R, Łukowski A, Baranowska M, Jagiełło R, Bułaj B, Hauke-Kowalska M, Szmyt J, Behnke JM, Robakowski P, Kowalkowski W. Variability of Functional Groups of Rhizosphere Fungi of Norway Spruce ( Picea abies (L.) H.Karst.) in the Boreal Range: The Wigry National Park, Poland. Int J Mol Sci 2023; 24:12628. [PMID: 37628809 PMCID: PMC10454689 DOI: 10.3390/ijms241612628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Rhizosphere microbial communities can influence plant growth and development. Natural regeneration processes take place in the tree stands of protected areas, which makes it possible to observe the natural changes taking place in the rhizosphere along with the development of the plants. This study aimed to determine the diversity (taxonomic and functional) of the rhizosphere fungal communities of Norway spruce growing in one of four developmental stages. Our research was based on the ITS region using Illumina system sequencing. Saprotrophs dominated in the studied rhizospheres, but their percentage share decreased with the age of the development group (for 51.91 from 43.13%). However, in the case of mycorrhizal fungi, an opposite trend was observed (16.96-26.75%). The most numerous genera were: saprotrophic Aspergillus (2.54-3.83%), Penicillium (6.47-12.86%), Pyrenochaeta (1.39-11.78%), pathogenic Curvularia (0.53-4.39%), and mycorrhizal Cortinarius (1.80-5.46%), Pseudotomentella (2.94-5.64%) and Tomentella (4.54-15.94%). The species composition of rhizosphere fungal communities was favorable for the regeneration of natural spruce and the development of multi-generational Norway spruce stands. The ratio of the abundance of saprotrophic and mycorrhizal fungi to the abundance of pathogens was high and promising for the durability of the large proportion of spruce in the Wigry National Park and for forest ecosystems in general.
Collapse
Affiliation(s)
- Jolanta Behnke-Borowczyk
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Robert Korzeniewicz
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Adrian Łukowski
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Marlena Baranowska
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Radosław Jagiełło
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Bartosz Bułaj
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Maria Hauke-Kowalska
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Janusz Szmyt
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Jerzy M. Behnke
- School of Life Sciences, University Park Nottingham, Nottingham NG7 2RD, UK;
| | - Piotr Robakowski
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Wojciech Kowalkowski
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| |
Collapse
|
27
|
Dong H, Sun H, Chen C, Zhang M, Ma D. Compositional Shifts and Assembly in Rhizosphere-Associated Fungal Microbiota Throughout the Life Cycle of Japonica Rice Under Increased Nitrogen Fertilization. RICE (NEW YORK, N.Y.) 2023; 16:34. [PMID: 37526797 PMCID: PMC10393908 DOI: 10.1186/s12284-023-00651-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
Soil fungal microbiomes facilitate a range of beneficial functions for their host plants, and rhizosphere fungal community composition, richness, and diversity affect plant growth and development, and crop yield. Therefore, exploring the community structure and assembly of the rhizosphere fungal microbiome and its relationship with soil biochemical properties are fundamental to elucidating how rice plants benefit from their fungal symbionts. In this study, soil samples were collected at seedling, tillering, heading, and ripening stages of rice subjected to three levels of nitrogen fertilization. Plant growth demonstrates a substantial influence on fungal community composition and diversity. From the tillering to the ripening stage, the fungal communities were governed by homogenizing dispersal and dispersal limitation. The prevalence of Glomeromycota, the beneficial fungi, was considerably higher during the heading stage compared to the three other growth stages. This increase in abundance was strongly associated with increased levels of soil nutrients and enhanced activity of nitrogen acquisition enzymes. This may be a strategy developed by rice grown in flooded soil to recruit beneficial fungi in the rhizosphere to meet high nitrogen demands. Our study findings contribute to elucidating the influence of plant development and nitrogen fertilization on the structure and composition of the fungal community as well as its relationship with soil key soil nutrient content and nitrogen-related enzyme activities. They also illustrate how a shift in the fungal community mediates and reflects the effects of nitrogen fertilization input in rice agroecosystems. These findings provide new insights into the effects of changes in nitrogen application in rice rhizosphere at different growth stages on fungal communities and soil biochemical characteristics.
Collapse
Affiliation(s)
- Hangyu Dong
- Key Laboratory of Northeast Rice Biology and Breeding, Rice Research Institute, Shenyang Agricultural University, Shenyang, China
- Agronomy College, Shenyang Agricultural University, Shenyang, China
| | - Haoyuan Sun
- Key Laboratory of Northeast Rice Biology and Breeding, Rice Research Institute, Shenyang Agricultural University, Shenyang, China
- Agronomy College, Shenyang Agricultural University, Shenyang, China
| | - Conglin Chen
- Key Laboratory of Northeast Rice Biology and Breeding, Rice Research Institute, Shenyang Agricultural University, Shenyang, China
- Agronomy College, Shenyang Agricultural University, Shenyang, China
| | - Mingyu Zhang
- Key Laboratory of Northeast Rice Biology and Breeding, Rice Research Institute, Shenyang Agricultural University, Shenyang, China
- Agronomy College, Shenyang Agricultural University, Shenyang, China
| | - Dianrong Ma
- Agronomy College, Liaodong University, Dandong, China.
| |
Collapse
|
28
|
Reyes-Martín MP, Fernández-Ondoño E, Ortiz-Bernad I, Abreu MM. Influence of Intensive and Super-Intensive Olive Grove Management on Soil Quality-Nutrients Content and Enzyme Activities. PLANTS (BASEL, SWITZERLAND) 2023; 12:2779. [PMID: 37570933 PMCID: PMC10421087 DOI: 10.3390/plants12152779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/18/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023]
Abstract
Agricultural soil quality is an issue that has been widely debated in the literature in recent decades. Three olive grove areas (one in Lisbon and the others in Santarém, Portugal) with different management techniques (intensive and super-intensive) were selected. Nutrient concentrations and enzyme activities of soils were determined, as well as the C and N of litter and pruning waste (mulch) to estimate the influence of management techniques on the quality of olive grove soils and to assess the extent to which they are affected by organic covers and different cultivation intensities. Organic C and total N concentrations in soils of the intensive olive grove in Lisbon were the highest when compared with those in the intensive and super-intensive olive groves soils of Santarém. The concentrations of Ca, Mg, Na, and K were the main differences between the Lisbon olive groves and the other two from Santarém. Phosphatase, cellulase, and urease activities were related to the Na, extractable K, extractable P, Zn, Mn, organic C, and total N soil concentrations. Soil management and agricultural practices are determining factors for these enzymatic activities of Santarém olive groves, although climate conditions and soil properties play an important role in the soil enzymatic activities.
Collapse
Affiliation(s)
- Marino Pedro Reyes-Martín
- Department of Soil Science and Agricultural Chemistry, Faculty of Science, University of Granada, Av. de Fuentenueva s/n, 18071 Granada, Spain; (E.F.-O.); (I.O.-B.)
| | - Emilia Fernández-Ondoño
- Department of Soil Science and Agricultural Chemistry, Faculty of Science, University of Granada, Av. de Fuentenueva s/n, 18071 Granada, Spain; (E.F.-O.); (I.O.-B.)
| | - Irene Ortiz-Bernad
- Department of Soil Science and Agricultural Chemistry, Faculty of Science, University of Granada, Av. de Fuentenueva s/n, 18071 Granada, Spain; (E.F.-O.); (I.O.-B.)
| | - Maria Manuela Abreu
- LEAF—Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), University of Lisbon, Tapada da Ajuda, 1349-017 Lisboa, Portugal;
| |
Collapse
|
29
|
Wei L, Zhao Q, Chen X, Sun Q, Zhang X, Chen Y. Seasonal variation in soil algal community structure in different forest plantations in subtropic China. FRONTIERS IN PLANT SCIENCE 2023; 14:1181184. [PMID: 37521936 PMCID: PMC10382206 DOI: 10.3389/fpls.2023.1181184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023]
Abstract
Algae exert great impact on soil formation and biogeochemical cycling. However, there is no full understanding of the response of soil algal community structure to the seasonal fluctuations in temperature and moisture and changes of soil physicochemical properties across different forests. Here, based on 23S rRNA gene sequencing, we analyzed soil algal community structure in four different forest plantations in two seasons and examined soil physiochemical properties. The results showed the significantly seasonal variation in soil algal community structure, with the higher overall diversity in summer than in winter. In addition, there existed significant correlations between soil algae (species composition, relative abundance, diversity index) and physicochemical properties (pH, total phosphorus, organic matter and nitrate nitrogen), suggesting that edaphic characteristics are also largely responsible for the variation in soil algal community. Nevertheless, the seasonal variation in algal community structure was greater than the variation across different forest plantations. This suggest temperature and moisture are more important than soil physicochemical properties in determining soil algal community structure. The findings of the present study enhance our understanding of the algal communities in forest ecosystems and are of great significance for the management and protection of algal ecosystem.
Collapse
Affiliation(s)
- Liman Wei
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China
- Agricultural Sensors and Intelligent Perception Technology Innovation Center of Anhui Province, Zhongke Hefei Institutes of Collaborative Research and Innovation for Intelligent Agriculture, Hefei, China
| | - Qiong Zhao
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China
| | - Xiangyu Chen
- Agricultural Sensors and Intelligent Perception Technology Innovation Center of Anhui Province, Zhongke Hefei Institutes of Collaborative Research and Innovation for Intelligent Agriculture, Hefei, China
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Qingye Sun
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China
| | - Xiang Zhang
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China
| | - Yongjing Chen
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China
| |
Collapse
|
30
|
Wang Z, Xu M, Li F, Bai Y, Hou J, Li X, Cao R, Deng Y, Jiang Y, Wang H, Yang W. Changes in soil bacterial communities and functional groups beneath coarse woody debris across a subalpine forest successional series. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
|
31
|
Bilański P, Jankowiak R, Solheim H, Fortuna P, Chyrzyński Ł, Warzecha P, Taerum SJ. Soil-borne Ophiostomatales species (Sordariomycetes, Ascomycota) in beech, oak, pine, and spruce stands in Poland with descriptions of Sporothrixroztoczensis sp. nov., S.silvicola sp. nov., and S.tumida sp. nov. MycoKeys 2023; 97:41-69. [PMID: 37251288 PMCID: PMC10210257 DOI: 10.3897/mycokeys.97.97416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/19/2023] [Indexed: 05/31/2023] Open
Abstract
Ophiostomatales (Ascomycota) contains many species, most of which are associated with bark beetles. Some members of this order are plant or animal pathogens, while others colonize soil, different plant tissues, or even carpophores of some Basidiomycota. However, little is known about soil-inhabiting Ophiostomatales fungi. A survey of these fungi associated with soil under beech, oak, pine, and spruce stands in Poland yielded 623 isolates, representing 10 species: Heinzbutiniagrandicarpa, Leptographiumprocerum, L.radiaticola, Ophiostomapiliferum, O.quercus, Sporothrixbrunneoviolacea, S.dentifunda, S.eucastaneae, and two newly described taxa, namely Sporothrixroztoczensissp. nov. and S.silvicolasp. nov. In addition, isolates collected from fallen shoots of Pinussylvestris that were pruned by Tomicus sp. are described as Sporothrixtumidasp. nov. The new taxa were morphologically characterized and phylogenetically analyzed based on multi-loci sequence data (ITS, β-tubulin, calmodulin, and translation elongation factor 1-α genes). The Ophiostomatales species were especially abundant in soil under pine and oak stands. Leptographiumprocerum, S.silvicola, and S.roztoczensis were the most frequently isolated species from soil under pine stands, while S.brunneoviolacea was the most abundant in soil under oak stands. The results highlight that forest soil in Poland has a wide diversity of Ophiostomatales taxa, but further studies are required to uncover the molecular diversity and phylogenetic relationships of these fungi, as well as their roles in soil fungal communities.
Collapse
Affiliation(s)
- Piotr Bilański
- Department of Forest Ecosystems Protection, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, PolandUniversity of Agriculture in KrakowKrakowPoland
| | - Robert Jankowiak
- Department of Forest Ecosystems Protection, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, PolandUniversity of Agriculture in KrakowKrakowPoland
| | - Halvor Solheim
- Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431, Ås, NorwayNorwegian Institute of Bioeconomy ResearchÅsNorway
| | - Paweł Fortuna
- Department of Forest Ecosystems Protection, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, PolandUniversity of Agriculture in KrakowKrakowPoland
| | - Łukasz Chyrzyński
- Department of Forest Ecosystems Protection, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, PolandUniversity of Agriculture in KrakowKrakowPoland
| | - Paulina Warzecha
- Department of Forest Ecosystems Protection, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, PolandUniversity of Agriculture in KrakowKrakowPoland
| | - Stephen Joshua Taerum
- The Connecticut Agricultural Experiment Station, Department of Plant Pathology and Ecology, Jenkins-Waggoner Laboratory, 123 Huntington Street P.O. Box 1106, New Haven, CT 06504-1106, USAThe Connecticut Agricultural Experiment Station, Department of Plant Pathology and Ecology, Jenkins-Waggoner LaboratoryNew HavenUnited States of America
| |
Collapse
|
32
|
Saraiva JP, Bartholomäus A, Toscan RB, Baldrian P, Nunes da Rocha U. Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes. Mol Ecol Resour 2023. [PMID: 36847735 DOI: 10.1111/1755-0998.13776] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 01/23/2023] [Accepted: 02/21/2023] [Indexed: 03/01/2023]
Abstract
As most eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although approaches to recovering Prokaryotic genomes have become common in genome biology, few studies have tackled the recovery of eukaryotic genomes from metagenomes. This study assessed the reconstruction of microbial eukaryotic genomes using 6000 metagenomes from terrestrial and some transition environments using the EukRep pipeline. Only 215 metagenomic libraries yielded eukaryotic bins. From a total of 447 eukaryotic bins recovered 197 were classified at the phylum level. Streptophytes and fungi were the most represented clades with 83 and 73 bins, respectively. More than 78% of the obtained eukaryotic bins were recovered from samples whose biomes were classified as host-associated, aquatic, and anthropogenic terrestrial. However, only 93 bins were taxonomically assigned at the genus level and 17 bins at the species level. Completeness and contamination estimates were obtained for a total of 193 bins and consisted of 44.64% (σ = 27.41%) and 3.97% (σ = 6.53%), respectively. Micromonas commoda was the most frequent taxon found while Saccharomyces cerevisiae presented the highest completeness, probably because more reference genomes are available. Current measures of completeness are based on the presence of single-copy genes. However, mapping of the contigs from the recovered eukaryotic bins to the chromosomes of the reference genomes showed many gaps, suggesting that completeness measures should also include chromosome coverage. Recovering eukaryotic genomes will benefit significantly from long-read sequencing, development of tools for dealing with repeat-rich genomes, and improved reference genomes databases.
Collapse
Affiliation(s)
- Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ GmbH, Leipzig, Germany
| | | | - Rodolfo Brizola Toscan
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ GmbH, Leipzig, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ GmbH, Leipzig, Germany
| |
Collapse
|
33
|
Lammel DR, Szymczak A, Bielcik M, Rillig MC. Fungal growth response to recurring heating events is modulated by species interactions. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.1028136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
An increasing frequency of heat events can affect key organisms related to ecosystem functions. Soil saprobic fungi have important roles in carbon and nutrient cycling in soils, and they are clearly affected by heat events. When tested individually, saprobic soil fungi showed a variety of growth responses to a series of two heat events. However, in nature, these fungi rarely grow alone. Coexistence theory predicts that diversity in the response to stressors can influence the outcome of species interactions and growth. This means that the co-cultivation of different fungi may affect their growth response to heat events. To test if recurring heat events affect fungal growth in small synthetic communities, we evaluated fungi previously known to respond to recurring heat events in experimental small communities composed of two and three species. For the fungi growing in pairs, surprisingly, most of the responses could not be predicted by how the isolates responded individually. In some cases, facilitation or increased competition was observed. For the three fungi growing together, results were also not predicted by the individual or pair responses. Both the heat events and the small communities influenced the growth of the fungi and growth properties emerged from the interactions among isolates and the heat stress. We show that not only do environmental conditions influence fungal interactions and growth rates but also that the co-cultivation of different fungi affects the fungal response to recurring heat events. These results indicate that more complex experimental designs are needed to better understand the effects of recurring heat events and climate change on soil fungi.
Collapse
|
34
|
Tanunchai B, Ji L, Schroeter SA, Wahdan SFM, Hossen S, Delelegn Y, Buscot F, Lehnert AS, Alves EG, Hilke I, Gleixner G, Schulze ED, Noll M, Purahong W. FungalTraits vs. FUNGuild: Comparison of Ecological Functional Assignments of Leaf- and Needle-Associated Fungi Across 12 Temperate Tree Species. MICROBIAL ECOLOGY 2023; 85:411-428. [PMID: 35124727 PMCID: PMC9958157 DOI: 10.1007/s00248-022-01973-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/21/2022] [Indexed: 05/16/2023]
Abstract
Recently, a new annotation tool "FungalTraits" was created based on the previous FUNGuild and FunFun databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)-based amplicon sequencing dataset on amplicon sequence variants (ASVs) were addressed. Sequencing dataset was derived from leaves and needles of 12 temperate broadleaved and coniferous tree species. We found that FungalTraits assigned more functional traits than FUNGuild, and especially the coverage of saprotrophs, plant pathogens, and endophytes was higher while lichenized fungi revealed similar findings. Moreover, ASVs derived from leaves and needles of each tree species were better assigned to all available fungal traits as well as to saprotrophs by FungalTraits compared to FUNGuild in particular for broadleaved tree species. Assigned ASV richness as well as fungal functional community composition was higher and more diverse after analyses with FungalTraits compared to FUNGuild. Moreover, datasets of both databases showed similar effect of environmental factors for saprotrophs but for endophytes, unidentical patterns of significant corresponding factors were obtained. As a conclusion, FungalTraits is superior to FUNGuild in assigning a higher quantity and quality of ASVs as well as a higher frequency of significant correlations with environmental factors.
Collapse
Affiliation(s)
- Benjawan Tanunchai
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Li Ji
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, 150040 Harbin, People’s Republic of China
| | - Simon Andreas Schroeter
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Botany Department, Faculty of Science, Suez Canal University, Ismailia, 41522 Egypt
| | - Shakhawat Hossen
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Yoseph Delelegn
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Ann-Sophie Lehnert
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Eliane Gomes Alves
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Ines Hilke
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Gerd Gleixner
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Ernst-Detlef Schulze
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Matthias Noll
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| |
Collapse
|
35
|
Vivelo S, Alsairafi B, Walsh JT, Bhatnagar JM. Intrinsic growth rate and cellobiohydrolase activity underlie the phylogenetic signal to fungal decomposer succession. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
36
|
Li B, Liu X, Zhu D, Su H, Guo K, Sun G, Li X, Sun L. Crop diversity promotes the recovery of fungal communities in saline-alkali areas of the Western Songnen Plain. Front Microbiol 2023; 14:1091117. [PMID: 36819047 PMCID: PMC9930164 DOI: 10.3389/fmicb.2023.1091117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023] Open
Abstract
Introduction Phytoremediation is an effective strategy for saline land restoration. In the Western Songnen Plain, northeast China, soil fungal community recovery for saline phytoremediation has not been well documented among different cropping patterns. In this study, we tested how rotation, mixture, and monoculture cropping patterns impact fungal communities in saline-alkali soils to assess the variability between cropping patterns. Methods The fungal communities of the soils of the different cropping types were determined using Illumina Miseq sequencing. Results Mixture and rotation promoted an increase in operational taxonomic unit (OTU) richness, and OTU richness in the mixture system decreased with increasing soil depth. A principal coordinate analysis (PCoA) showed that cropping patterns and soil depths influenced the structure of fungal communities, which may be due to the impact of soil chemistry. This was reflected by soil total nitrogen (TN) and electrical conductivity (EC) being the key factors driving OTU richness, while soil available potassium (AK) and total phosphorus (TP) were significantly correlated with the relative abundance of fungal dominant genus. The relative abundance of Leptosphaerulina, Alternaria, Myrothecium, Gibberella, and Tetracladium varied significantly between cropping patterns, and Leptosphaerulina was significantly associated with soil chemistry. Soil depth caused significant differences in the relative abundance of Fusarium in rotation and mixture soils, with Fusarium more commonly active at 0-15 cm deep soil. Null-model analysis revealed that the fungal community assembly of the mixture soils in 0-15 cm deep soil was dominated by deterministic processes, unlike the other two cropping patterns. Furthermore, fungal symbiotic networks were more complex in rotation and mixture than in monoculture soils, reflected in more nodes, more module hubs, and connectors. The fungal networks in rotation and mixture soils were more stable than in monoculture soils, and mixture networks were obviously more connected than rotations. FUNGuild showed that the relative proportion of saprotroph in rotation and mixture was significantly higher than that in monocultures. The highest proportion of pathotroph and symbiotroph was exhibited in rotation and mixture soils, respectively. Discussion Overall, mixture is superior to crop rotation and monocultures in restoring fungal communities of the saline-alkali soils of the Western Songnen Plain, northeast China.
Collapse
Affiliation(s)
- Bin Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Xiaoqian Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Dan Zhu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Heng Su
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Kaiwen Guo
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Guangyu Sun
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Xin Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China,School of Forestry, Northeast Forestry University, Harbin, China,*Correspondence: Xin Li, ✉
| | - Lei Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, China,Lei Sun, ✉
| |
Collapse
|
37
|
Linking processes to community functions—insights into litter decomposition combining fungal metatranscriptomics and environmental NMR profiling. Mycol Prog 2023. [DOI: 10.1007/s11557-022-01859-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
AbstractIn forest ecosystems, decomposition is essential for carbon and nutrient cycling and therefore a key process for ecosystem functioning. During the decomposition process, litter chemistry, involved decomposer organisms, and enzymatic activity change interdependently. Chemical composition of the litter is the most complex and dynamic component in the decomposition process and therefore challenging to assess holistically. In this study, we aimed to characterize chemical shifts during decomposition and link them to changes in decomposer fungal activity. We characterized the chemical composition of freshly fallen autumn leaves of European beech (Fagus sylvatica) and the corresponding leaf litter after 1 year of decomposition by proton nuclear magnetic resonance spectroscopy. We further tested the applicability of spiking experiments for qualitative and quantitative characterization of leaves and litter chemistry. The composition and transcriptional activity of fungal communities was assessed by high-throughput Illumina sequencing in the same litter samples. We were able to distinguish freshly fallen leaves from 1-year-old litter based on their chemical composition. Chemical composition of leaves converged among regions with progressing decomposition. Fungal litter communities differed in composition among regions, but they were functionally redundant according to the expression of genes encoding litter degrading enzymes (CAZymes). Fungi of the saprotrophic genera Mycena and Chalara correlated with transcription of litter-degrading CAZymes in 1-year-old litter. Forestry measures influenced the diversity and transcription rate of the detected CAZymes transcripts in litter. Their expression was primarily predicted by composition of the soluble chemical fraction of the litter. Environmental NMR fingerprints thus proved valuable for inferring ecological contexts. We propose and discuss a holistic framework to link fungal activity, enzyme expression, and chemical composition.
Collapse
|
38
|
Langrand J, Lounès-Hadj Sahraoui A, Duclercq J, Raveau R, Laruelle F, Bert V, Facon N, Tisserant B, Fontaine J. Coriander ( Coriandrum sativum) Cultivation Combined with Arbuscular Mycorrhizal Fungi Inoculation and Steel Slag Application Influences Trace Elements-Polluted Soil Bacterial Functioning. PLANTS (BASEL, SWITZERLAND) 2023; 12:618. [PMID: 36771702 PMCID: PMC9920375 DOI: 10.3390/plants12030618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
The cultivation of aromatic plants for the extraction of essential oils has been presented as an innovative and economically viable alternative for the remediation of areas polluted with trace elements (TE). Therefore, this study focuses on the contribution of the cultivation of coriander and the use of arbuscular mycorrhizal fungi (AMF) in combination with mineral amendments (steel slag) on the bacterial function of the rhizosphere, an aspect that is currently poorly understood and studied. The introduction of soil amendments, such as steel slag or mycorrhizal inoculum, had no significant effect on coriander growth. However, steel slag changed the structure of the bacterial community in the rhizosphere without affecting microbial function. In fact, Actinobacteria were significantly less abundant under slag-amended conditions, while the relative proportion of Gemmatimonadota increased. On the other hand, the planting of coriander affects the bacterial community structure and significantly increased the bacterial functional richness of the amended soil. Overall, these results show that planting coriander most affected the structure and functioning of bacterial communities in the TE-polluted soils and reversed the effects of mineral amendments on rhizosphere bacterial communities and their activities. This study highlights the potential of coriander, especially in combination with steel slag, for phytomanagement of TE-polluted soils, by improving soil quality and health.
Collapse
Affiliation(s)
- Julien Langrand
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Anissa Lounès-Hadj Sahraoui
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Jérôme Duclercq
- Unité Écologie et Dynamique des Systèmes Anthropisés (EDYSAN UMR CNRS 7058 CNRS), Université de Picardie Jules Verne, UFR des Sciences, 80029 Amiens, France
| | - Robin Raveau
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), UMR Santé et Agroécologie du Vignoble (SAVE), Bordeaux Sciences Agro, ISVV, 33882 Villenave d’Ornon, France
| | - Frédéric Laruelle
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Valérie Bert
- Unité Technologies Propres et Economie Circulaire, INERIS, Parc Technologique Alata, BP2, 60550 Verneuil en Halatte, France
| | - Natacha Facon
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Benoît Tisserant
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Joël Fontaine
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| |
Collapse
|
39
|
Mason AR, Taylor LS, DeBruyn JM. Microbial ecology of vertebrate decomposition in terrestrial ecosystems. FEMS Microbiol Ecol 2023; 99:6985004. [PMID: 36631293 DOI: 10.1093/femsec/fiad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/13/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Vertebrate decomposition results in an ephemeral disturbance of the surrounding environment. Microbial decomposers are recognized as key players in the breakdown of complex organic compounds, controlling carbon and nutrient fate in the ecosystem and potentially serving as indicators of time since death for forensic applications. As a result, there has been increasing attention on documenting the microbial communities associated with vertebrate decomposition, or the 'necrobiome'. These necrobiome studies differ in the vertebrate species, microhabitats (e.g. skin vs. soil), and geographic locations studied, but many are narrowly focused on the forensic application of microbial data, missing the larger opportunity to understand the ecology of these communities. To further our understanding of microbial dynamics during vertebrate decomposition and identify knowledge gaps, there is a need to assess the current works from an ecological systems perspective. In this review, we examine recent work pertaining to microbial community dynamics and succession during vertebrate (human and other mammals) decomposition in terrestrial ecosystems, through the lens of a microbial succession ecological framework. From this perspective, we describe three major microbial microhabitats (internal, external, and soil) in terms of their unique successional trajectories and identify three major knowledge gaps that remain to be addressed.
Collapse
Affiliation(s)
- Allison R Mason
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
| | - Lois S Taylor
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996, United States
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996, United States
| |
Collapse
|
40
|
Kalntremtziou M, Papaioannou IA, Vangalis V, Polemis E, Pappas KM, Zervakis GI, Typas MA. Evaluation of the lignocellulose degradation potential of Mediterranean forests soil microbial communities through diversity and targeted functional metagenomics. Front Microbiol 2023; 14:1121993. [PMID: 36922966 PMCID: PMC10008878 DOI: 10.3389/fmicb.2023.1121993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/31/2023] [Indexed: 02/28/2023] Open
Abstract
The enzymatic arsenal of several soil microorganisms renders them particularly suitable for the degradation of lignocellulose, a process of distinct ecological significance with promising biotechnological implications. In this study, we investigated the spatiotemporal diversity and distribution of bacteria and fungi with 16S and Internally Trascribed Spacer (ITS) ribosomal RNA next-generation-sequencing (NGS), focusing on forest mainland Abies cephalonica and insular Quercus ilex habitats of Greece. We analyzed samples during winter and summer periods, from different soil depths, and we applied optimized and combined targeted meta-omics approaches aiming at the peroxidase-catalase family enzymes to gain insights into the lignocellulose degradation process at the soil microbial community level. The microbial communities recorded showed distinct patterns of response to season, soil depth and vegetation type. Overall, in both forests Proteobacteria, Actinobacteria, Acidobacteria were the most abundant bacteria phyla, while the other phyla and the super-kingdom of Archaea were detected in very low numbers. Members of the orders Agaricales, Russulales, Sebacinales, Gomphales, Geastrales, Hysterangiales, Thelephorales, and Trechisporales (Basidiomycota), and Pezizales, Sordariales, Eurotiales, Pleosporales, Helotiales, and Diaporthales (Ascomycota) were the most abundant for Fungi. By using optimized "universal" PCR primers that targeted the peroxidase-catalase enzyme family, we identified several known and novel sequences from various Basidiomycota, even from taxa appearing at low abundance. The majority of the sequences recovered were manganese peroxidases from several genera of Agaricales, Hysterangiales, Gomphales, Geastrales, Russulales, Hymenochaetales, and Trechisporales, while lignin -and versatile-peroxidases were limited to two to eight species, respectively. Comparisons of the obtained sequences with publicly available data allowed a detailed structural analysis of polymorphisms and functionally relevant amino-acid residues at phylogenetic level. The targeted metagenomics applied here revealed an important role in lignocellulose degradation of hitherto understudied orders of Basidiomycota, such as the Hysterangiales and Gomphales, while it also suggested the auxiliary activity of particular members of Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes. The application of NGS-based metagenomics approaches allows a better understanding of the complex process of lignocellulolysis at the microbial community level as well as the identification of candidate taxa and genes for targeted functional investigations and genetic modifications.
Collapse
Affiliation(s)
- Maria Kalntremtziou
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis A Papaioannou
- Zentrum für Molekulare Biologie der Universität Heidelberg, ZMBH, University of Heidelberg, Heidelberg, Germany
| | - Vasileios Vangalis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Elias Polemis
- Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
| | - Katherine M Pappas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios I Zervakis
- Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
| | - Milton A Typas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
41
|
Hofmann B, Dreyling L, Dal Grande F, Otte J, Schmitt I. Habitat and tree species identity shape aboveground and belowground fungal communities in central European forests. Front Microbiol 2023; 14:1067906. [PMID: 36950169 PMCID: PMC10025312 DOI: 10.3389/fmicb.2023.1067906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
Introduction Trees interact with fungi in mutualistic, saprotrophic, and pathogenic relationships. With their extensive aboveground and belowground structures, trees provide diverse habitats for fungi. Thus, tree species identity is an important driver of fungal community composition in forests. Methods Here we investigate how forest habitat (bark surface vs. soil) and tree species identity (deciduous vs. coniferous) affect fungal communities in two Central European forests. We assess differences and interactions between fungal communities associated with bark surfaces and soil, in forest plots dominated either by Fagus sylvatica, Picea abies, or Pinus sylvestris in two study regions in southwestern and northeastern Germany. Results ITS metabarcoding yielded 3,357 fungal amplicon sequence variants (ASVs) in the northern and 6,088 in the southern region. Overall, soil communities were 4.7 times more diverse than bark communities. Habitat type explained 48-69% of the variation in alpha diversity, while tree species identity explained >1-3%. NMDS ordinations showed that habitat type and host tree species structured the fungal communities. Overall, few fungal taxa were shared between habitats, or between tree species, but the shared taxa were highly abundant. Network analyses, based on co-occurrence patterns, indicate that aboveground and belowground communities form distinct subnetworks. Discussion Our study suggests that habitat (bark versus soil) and tree species identity are important factors structuring fungal communities in temperate European forests. The aboveground (bark-associated) fungal community is currently poorly known, including a high proportion of reads assigned to "unknown Ascomycota" or "unknown Dothideomycetes." The role of bark as a habitat and reservoir of unique fungal diversity in forests has been underestimated.
Collapse
Affiliation(s)
- Benjamin Hofmann
- Institute of Ecology, Diversity and Evolution, Goethe University Frankfurt, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Lukas Dreyling
- Institute of Ecology, Diversity and Evolution, Goethe University Frankfurt, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
- Department of Biology, University of Padova, Padua, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Imke Schmitt
- Institute of Ecology, Diversity and Evolution, Goethe University Frankfurt, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
- *Correspondence: Imke Schmitt,
| |
Collapse
|
42
|
Štursová M, López-Mondéjar R, Baldrian P. Investigating the Bacterial and Fungal Communities Involved in Dead Biomass Degradation in Forest Soils. Methods Mol Biol 2022; 2605:157-168. [PMID: 36520393 DOI: 10.1007/978-1-0716-2871-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Stable isotope probing (SIP) provides the opportunity to label decomposer microorganisms that build their biomass on a specific substrate. In combination with high-throughput sequencing, SIP allows for the identification of microbial community members involved in a particular decomposition process. Further information can be gained (in SIP experiments) through gene-targeted metagenomics and metatranscriptomics, opening the possibility to describe the pool of genes catalyzing specific decomposition reactions in situ and to identify the diversity of genes that are expressed. When combined with gene descriptions of fungal and/or bacterial isolates from the same environment, specific biochemical reactions involved in decomposition can be linked to individual microbial taxa. Here, we describe the use of these methods to explore the decomposer community of fungi and bacteria in forest litter and soil.
Collapse
Affiliation(s)
- Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Ruben López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic.
| |
Collapse
|
43
|
Substrate and low intensity fires influence bacterial communities in longleaf pine savanna. Sci Rep 2022; 12:20904. [PMID: 36463255 PMCID: PMC9719495 DOI: 10.1038/s41598-022-24896-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/22/2022] [Indexed: 12/04/2022] Open
Abstract
Bacterial communities associated with vegetation-soil interfaces have important roles in terrestrial ecosystems. These bacterial communities, studied almost exclusively in unburnt ecosystems or those affected by rare, high-intensity wildfires, have been understudied in fire-frequented grasslands and savannas. The composition of ground-level bacterial communities was explored in an old-growth pine savanna with a centuries-long management history of prescribed fires every 1-2 years. Using 16S metabarcoding, hypotheses were tested regarding differences in bacterial families of litter and soil surface substrates in patches of ground layer vegetation that were naturally burnt or unburnt during landscape-level prescribed fires. Litter/soil substrates and fire/no fire treatments explained 67.5% of bacterial community variation and differences, driven by relative abundance shifts of specific bacterial families. Fires did not strongly affect plant or soil variables, which were not linked to bacterial community differences. Litter/soil substrates and the naturally patchy frequent fires appear to generate microhabitat heterogeneity in this pine savanna, driving responses of bacterial families. Prescribed fire management may benefit from considering how fire-altered substrate heterogeneity influences and maintains microbial diversity and function, especially in these fiery ecosystems. Frequent, low-intensity fires appear ecologically important in maintaining the diverse microbial foundation that underlie ecosystem processes and services in fire-frequented habitats.
Collapse
|
44
|
Wang F, Kong W, Ji M, Zhao K, Chen H, Yue L, Dong X. Grazing greatly reduces the temporal stability of soil cellulolytic fungal community in a steppe on the Tibetan Plateau. J Environ Sci (China) 2022; 121:48-57. [PMID: 35654515 DOI: 10.1016/j.jes.2021.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/18/2021] [Accepted: 09/18/2021] [Indexed: 06/15/2023]
Abstract
Excessive livestock grazing degrades grasslands ecosystem stability and sustainability by reducing soil organic matter and plant productivity. However, the effects of grazing on soil cellulolytic fungi, an important indicator of the degradation process for soil organic matter, remain less well understood. Using T-RFLP and sequencing methods, we investigated the effects of grazing on the temporal changes of cellulolytic fungal abundance and community structure in dry steppe soils during the growing months from May to September, on the Tibetan Plateau using T-RFLP and sequencing methods. The results demonstrated that the abundance of soil cellulolytic fungi under grazing treatment changed significantly from month to month, and was positively correlated with dissolved organic carbon (DOC) and soil temperature, but negatively correlated with soil pH. Contrastingly, cellulolytic fungal abundance did not change within the fencing treatment (ungrazed conditions). Cellulolytic fungal community structure changed significantly in the growing months in grazed soils, but did not change in fenced soils. Grazing played a key role in determining the community structure of soil cellulolytic fungi by explaining 8.1% of the variation, while pH and DOC explained 4.1% and 4.0%, respectively. Phylogenetically, the cellulolytic fungi were primarily affiliated with Ascomycota (69.65% in relative abundance) and Basidiomycota (30.35%). Therefore, grazing substantially reduced the stability of soil cellulolytic fungal abundance and community structure, as compared with the fencing treatment. Our finding provides a new insight into the responses of organic matter-decomposing microbes for grassland managements.
Collapse
Affiliation(s)
- Fei Wang
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, China.
| | - Mukan Ji
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Kang Zhao
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; School of Life Science, Shanxi Normal University, Linfen 041004, China
| | - Hao Chen
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Linyan Yue
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xiaobin Dong
- State Key Laboratory of Earth Surface Processes and Resource Ecology, College of Resources Science and Technology, Beijing Normal University, Beijing 100875, China
| |
Collapse
|
45
|
Parada-Pozo G, Bravo LA, Sáez PL, Cavieres LA, Reyes-Díaz M, Abades S, Alfaro FD, De la Iglesia R, Trefault N. Vegetation drives the response of the active fraction of the rhizosphere microbial communities to soil warming in Antarctic vascular plants. FEMS Microbiol Ecol 2022; 98:6679102. [PMID: 36040342 DOI: 10.1093/femsec/fiac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/11/2022] [Accepted: 08/27/2022] [Indexed: 01/21/2023] Open
Abstract
In the Antarctic Peninsula, increases in mean annual temperature are associated with the coverage and population density of the two Antarctic vascular plant species-Deschampsia antarctica and Colobanthus quitensis-potentially modifying critical soil processes. In this study, we characterized the diversity and community composition of active microorganisms inhabiting the vascular plant rhizosphere in two sites with contrasting vegetation cover in King George Island, Western Antarctic Peninsula. We assessed the interplay between soil physicochemical properties and microbial diversity and composition, evaluating the effect of an in situ experimental warming on the microbial communities of the rhizosphere from D. antarctica and C. quitensis. Bacteria and Eukarya showed different responses to warming in both sites, and the effect was more noticeable in microbial eukaryotes from the low vegetation site. Furthermore, important changes were found in the relative abundance of Tepidisphaerales (Bacteria) and Ciliophora (Eukarya) between warming and control treatments. Our results showed that rhizosphere eukaryal communities are more sensitive to in situ warming than bacterial communities. Overall, our results indicate that vegetation drives the response of the active fraction of the microbial communities from the rhizosphere of Antarctic vascular plants to soil warming.
Collapse
Affiliation(s)
- Génesis Parada-Pozo
- Centro GEMA-Genómica, Ecología & Medio Ambiente, Facultad de Ciencias, Universidad Mayor, 8580745, Santiago, Chile
| | - León A Bravo
- Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera. 4811230, Temuco, Chile
| | - Patricia L Sáez
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción, 4070386, Chile.,Instituto de Ecología y Biodiversidad (IEB), 775000, Santiago, Chile
| | - Lohengrin A Cavieres
- Instituto de Ecología y Biodiversidad (IEB), 775000, Santiago, Chile.,Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, 4070386, Chile
| | - Marjorie Reyes-Díaz
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, 4811230, Chile.,Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, 4811230, Chile
| | - Sebastián Abades
- Centro GEMA-Genómica, Ecología & Medio Ambiente, Facultad de Ciencias, Universidad Mayor, 8580745, Santiago, Chile
| | - Fernando D Alfaro
- Centro GEMA-Genómica, Ecología & Medio Ambiente, Facultad de Ciencias, Universidad Mayor, 8580745, Santiago, Chile
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8320000, Chile
| | - Nicole Trefault
- Centro GEMA-Genómica, Ecología & Medio Ambiente, Facultad de Ciencias, Universidad Mayor, 8580745, Santiago, Chile
| |
Collapse
|
46
|
Martinović T, Kohout P, López-Mondéjar R, Algora Gallardo C, Starke R, Tomšovský M, Baldrian P. Bacterial community in soil and tree roots of Picea abies shows little response to clearcutting. FEMS Microbiol Ecol 2022; 98:6754320. [PMID: 36208910 DOI: 10.1093/femsec/fiac118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/15/2022] [Accepted: 10/06/2022] [Indexed: 01/21/2023] Open
Abstract
Clearcutting represents a standard management practice in temperate forests with dramatic consequences for the forest ecosystem. The removal of trees responsible for the bulk of primary production can result in a complex response of the soil microbiome. While studies have shown that tree root-symbiotic ectomycorrhizal fungi disappear from soil and decomposing fine roots of trees become a hotspot for fungal decomposition, the fate of the bacterial component of the soil microbiome following clearcutting is unclear. Here, we investigated the response of bacterial community composition for 2 years following clearcutting of a Picea abies stand in soil, rhizosphere and tree roots, by 16S rRNA amplicon sequencing. While in the first few months after clearcutting there was no significant response of bacterial community composition in the rhizosphere and soil, bacterial communities associated with tree roots underwent more profound changes over time. Acidobacteria were abundant in rhizosphere and soil, while Firmicutes were strongly represented in the roots. In addition, bacterial communities on decomposing roots were significantly different from those on pre-clearcut live roots. Compared with fungi, the response of bacterial communities to clearcutting was much less pronounced, indicating independent development of the two microbial domains.
Collapse
Affiliation(s)
- Tijana Martinović
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Faculty of Science, Charles University in Prague, Albertov 6, 128 00, Praha 2, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Faculty of Science, Charles University in Prague, Albertov 6, 128 00, Praha 2, Czech Republic
| | - Rubén López-Mondéjar
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Camelia Algora Gallardo
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Robert Starke
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Michal Tomšovský
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| |
Collapse
|
47
|
Jiang C, Liu Y, Li H, Zhu S, Sun X, Wu K, Shui W. The characterization of microbial communities and associations in karst tiankeng. Front Microbiol 2022; 13:1002198. [PMID: 36338100 PMCID: PMC9632645 DOI: 10.3389/fmicb.2022.1002198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/01/2022] [Indexed: 11/22/2022] Open
Abstract
The karst tiankeng is a special and grand negative terrain on the surface, that maintains a unique ecosystem. However, knowledge about bacterial and fungal communities in karst tiankengs is still limited. Therefore, soil samples from five karst tiankengs were collected and subjected to high-throughput sequencing of 16S rRNA and ITS genes, and multivariate statistical analysis. The results showed abundant and diversified bacterial and fungal communities in karst tiankeng. The bacterial communities were dominated by Proteobacteria and Acidobacteria, and the fungal communities were dominated by Ascomycota and Basidiomycota. Statistical analysis revealed significant differences in bacterial and fungal communities among the five karst tiankengs, which may indicate that the distribution of bacterial and fungal communities was driven by separate karst tiankengs. The co-occurrence network structure was characterized by highly modularized assembly patterns and more positive interactions. The keystone taxa were mainly involved in nutrient cycling and energy metabolism. The null model analysis results showed that the stochastic process, especially dispersal limitation, tended to be more important in controlling the development of bacterial and fungal communities in karst tiankeng. The bacterial community structure was significantly associated with soil properties (SWC, TN, AN, and BD), while the fungal community structure was significantly associated with soil properties (SWC and TP) and plant diversity. These results can expand our knowledge of the karst tiankeng microbiome.
Collapse
Affiliation(s)
- Cong Jiang
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yuanmeng Liu
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China
| | - Hui Li
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China
| | - Sufeng Zhu
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Xiang Sun
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China
| | - Kexing Wu
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China
| | - Wei Shui
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China
- *Correspondence: Wei Shui,
| |
Collapse
|
48
|
Luo X, Ye X, Wang W, Chen Y, Li Z, Wang Y, Huang Y, Ran W, Cao H, Cui Z. Temporal dynamics of total and active root-associated diazotrophic communities in field-grown rice. Front Microbiol 2022; 13:1016547. [PMID: 36312965 PMCID: PMC9606772 DOI: 10.3389/fmicb.2022.1016547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/23/2022] [Indexed: 11/26/2022] Open
Abstract
Plant-associated nitrogen-fixing microorganisms (diazotrophs) are essential to host nutrient acquisition, productivity and health, but how host growth affects the succession characteristics of crop diazotrophic communities is still poorly understood. Here, Illumina sequencing of DNA- and RNA-derived nifH genes was employed to investigate the dynamics of total and active diazotrophic communities across rhizosphere soil and rice roots under four fertilization regimes during three growth periods (tillering, heading and mature stages) of rice in 2015 and 2016. Our results indicated that 71.9–77.2% of the operational taxonomic units (OTUs) were both detected at the DNA and RNA levels. According to the nonmetric multidimensional scaling ordinations of Bray–Curtis distances, the variations in community composition of active rhizosphere diazotrophs were greater than those of total rhizosphere diazotrophs. The community composition (β-diversity) of total and active root-associated diazotrophs was shaped predominantly by microhabitat (niche; R2 ≥ 0.959, p < 0.001), followed by growth period (R2 ≥ 0.15, p < 0.001). The growth period had a stronger effect on endophytic diazotrophs than on rhizosphere diazotrophs. From the tillering stage to the heading stage, the α-diversity indices (Chao1, Shannon and phylogenetic diversity) and network topological parameters (edge numbers, average clustering coefficient and average degree values) of total endophytic diazotrophic communities increased. The proportions of OTUs shared by the total rhizosphere and endophytic diazotrophs in rhizosphere diazotrophs gradually increased during rice growth. Moreover, total diazotrophic α-diversity and network complexity decreased from rhizosphere soil to roots. Collectively, compared with total diazotrophic communities, active diazotrophic communities were better indicators of biological response to environmental changes. The host microhabitat profoundly drove the temporal dynamics of total and active root-associated diazotrophic communities, followed by the plant growth period.
Collapse
Affiliation(s)
- Xue Luo
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Zhongli Cui, , ; Xianfeng Ye,
| | - Wenhui Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yang Chen
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Yanxin Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Wei Ran
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Zhongli Cui, , ; Xianfeng Ye,
| |
Collapse
|
49
|
Travadon R, Lawrence DP, Moyer MM, Fujiyoshi PT, Baumgartner K. Fungal species associated with grapevine trunk diseases in Washington wine grapes and California table grapes, with novelties in the genera Cadophora, Cytospora, and Sporocadus. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:1018140. [PMID: 37746176 PMCID: PMC10512239 DOI: 10.3389/ffunb.2022.1018140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/09/2022] [Indexed: 09/26/2023]
Abstract
Grapevine trunk diseases cause serious economic losses to grape growers worldwide. The identification of the causal fungi is critical to implementing appropriate management strategies. Through a culture-based approach, we identified the fungal species composition associated with symptomatic grapevines from wine grapes in southeastern Washington and table grapes in the southern San Joaquin Valley of California, two regions with contrasting winter climates. Species were confirmed through molecular identification, sequencing two to six gene regions per isolate. Multilocus phylogenetic analyses were used to identify novel species. We identified 36 species from 112 isolates, with a combination of species that are new to science, are known causal fungi of grapevine trunk diseases, or are known causal fungi of diseases of other woody plants. The novel species Cadophora columbiana, Cytospora macropycnidia, Cytospora yakimana, and Sporocadus incarnatus are formally described and introduced, six species are newly reported from North America, and grape is reported as a new host for three species. Six species were shared between the two regions: Cytospora viticola, Diatrype stigma, Diplodia seriata, Kalmusia variispora, Phaeoacremonium minimum, and Phaeomoniella chlamydospora. Dominating the fungal community in Washington wine grape vineyards were species in the fungal families Diatrypaceae, Cytosporaceae and Sporocadaceae, whereas in California table grape vineyards, the dominant species were in the families Diatrypaceae, Togniniaceae, Phaeomoniellaceae and Hymenochaetaceae. Pathogenicity tests demonstrated that 10 isolates caused wood discoloration similar to symptomatic wood from which they were originally isolated. Growth rates at temperatures from 5 to 35°C of 10 isolates per region, suggest that adaptation to local climate might explain their distribution.
Collapse
Affiliation(s)
- Renaud Travadon
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Daniel P. Lawrence
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Michelle M. Moyer
- Department of Horticulture, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, United States
| | - Phillip T. Fujiyoshi
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture – Agricultural Research Service, Davis, CA, United States
| | - Kendra Baumgartner
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture – Agricultural Research Service, Davis, CA, United States
| |
Collapse
|
50
|
Mombrikotb SB, Van Agtmaal M, Johnstone E, Crawley MJ, Gweon HS, Griffiths RI, Bell T. The interactions and hierarchical effects of long-term agricultural stressors on soil bacterial communities. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:711-718. [PMID: 35925021 PMCID: PMC9804416 DOI: 10.1111/1758-2229.13106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 06/19/2022] [Indexed: 06/17/2023]
Abstract
Soils are subjected to multiple anthropogenic modifications, but the synergistic impacts of simultaneous environmental stressors on below-ground communities are poorly understood. We used a large-scale (1152 plots), long-term (26 years), multi-factorial grassland experiment to assess the impact of five common agricultural practises (pesticides, herbicide, liming, fertilizers and grazing exclusion) and their interactive effects on the composition and activity of soil microbial communities. We confirmed that pH strongly impacts belowground communities, but further demonstrate that pH strongly mediates the impacts of other management factors. Notably, there was a significant interaction between liming and the effect of pesticide application, with only half of the taxa responding to pesticide being shared in both limed and unlimed treatments. Likewise, nutrient amendments significantly altered bacterial community structure in acidic soils. Not only do these results highlight an hierarchy of effect of commonly used agricultural practices but also the widespread interactions between treatments: many taxa were significantly affected by interactions between treatments, even in the absence of significant main effects. Furthermore, the results demonstrated that chemical amendments may not percolate deeply into physically unperturbed soils with effects concentrated between 0 and 30 cm, despite 20+ years of treatment. The research shows that future changes to agricultural practices will need to consider interactions among multiple factors.
Collapse
Affiliation(s)
| | - Maaike Van Agtmaal
- Department of Life SciencesImperial College London, AscotBerkshireUK
- Louis Bolk InstituutBunnikThe Netherlands
| | - Emma Johnstone
- Department of Life SciencesImperial College London, AscotBerkshireUK
- School of Life SciencesUniversity of WarwickCoventryUK
| | | | - Hyun S. Gweon
- School of Biological SciencesUniversity of Reading, WhiteknightsReadingUK
- UK Centre of Ecology & HydrologyBangorUK
| | | | - Thomas Bell
- Department of Life SciencesImperial College London, AscotBerkshireUK
| |
Collapse
|