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Qin Z, Wang S, Wu Y, Sun J, Zhao F. Seasonal dynamics of intestinal microbiota in juvenile Chinese mitten crab ( Eriocheir sinensis) in the Yangtze Estuary. Front Cell Infect Microbiol 2024; 14:1436547. [PMID: 39027136 PMCID: PMC11254619 DOI: 10.3389/fcimb.2024.1436547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/13/2024] [Indexed: 07/20/2024] Open
Abstract
Introduction In this study, the seasonal differences in the intestinal microbiota of Chinese mitten crab (Eriocheir sinensis) larvae were investigated at different sites in the intertidal zone of the Yangtze River Estuary. Methods 16S rRNA high-throughput sequencing technology was used to compare and analyze the microbial community structure in the intestines of juvenile crab from different seasons. Results The results showed that the main microbial phyla in all seasons and sites were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, which accounted for 97.1% of the total microbiota. Composition analysis revealed that the relative abundance of Proteobacteria decreased from summer to winter at each station, whereas Bacteroidetes showed the opposite trend. Alpha diversity analysis showed that species richness increased from summer to winter at the upstream site (P < 0.05), but decreased at the downstream site (P < 0.05), with no significant differences observed in other comparisons. Biomarker species analysis showed that juvenile crab exhibited a more specialized microbial community in summer compared with autumn and winter. Co-occurrence network analysis revealed that microbial interaction network complexity was lower in autumn compared with summer and autumn. Functional prediction analysis showed that the microbial community only exhibited seasonal differences in amino acid biosynthesis, cofactor, prosthetic group, electron carrier, and vitamin biosynthesis, aromatic compound degradation, nucleotide and nucleoside degradation, and tricarboxylic acid cycle pathways. Discussion The results indicated that the microbiota did not significantly differ among sites, and seasonal variation was a main factor influencing the differences in intestinal microbiota of Chinese mitten juvenile crab. Moreover, the microbial community was more complex in summer compared with autumn and winter.
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Affiliation(s)
- Ze Qin
- College of Fisheries, Tianjin Agricultural University, Tianjin, China
- East China Sea Fisherises Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Sikai Wang
- East China Sea Fisherises Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
- Shanghai Yangtze River Estuary Fishery Resources Enhancement and Ecological Restoration Engineering and Technology Research, Shanghai, China
| | - Yeling Wu
- East China Sea Fisherises Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
- Shanghai Yangtze River Estuary Fishery Resources Enhancement and Ecological Restoration Engineering and Technology Research, Shanghai, China
| | - Jinhui Sun
- College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Feng Zhao
- East China Sea Fisherises Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
- Shanghai Yangtze River Estuary Fishery Resources Enhancement and Ecological Restoration Engineering and Technology Research, Shanghai, China
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Mateos DM, Bhatnagar JM. Restoring ecological complexity in a changing environment. Curr Biol 2024; 34:R365-R371. [PMID: 38714167 DOI: 10.1016/j.cub.2024.03.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
Abstract
As land use leaves massive tracts of land vacant for recovery, restoration must undergo a substantial shift to incorporate a complexity perspective beyond the traditional community, biodiversity or functional views. With an interaction-function perspective, we may be able to achieve ecosystems with better chances to adapt to current environmental changes and, especially, to climate change. We explore combined approaches that include still unused and underexplored techniques that will soon go mainstream and produce massive amounts of information to address the complexity gap. As we understand how complexity reassembles after the end of agriculture, we will be able to design actions to restore or enhance it at unprecedented spatial scales while increasing its adaptability to environmental changes.
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Affiliation(s)
- David Moreno Mateos
- School of Geography and the Environment, University of Oxford, Oxford OX1 3QY, UK; Basque Centre for Climate Change (BC3), Leioa 48940, Spain; Ikerbasque Foundation, Bilbao 48009, Spain.
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Yang M, Zhao L, Yu X, Shu W, Cao F, Liu Q, Liu M, Wang J, Jiang Y. Microbial community structure and co-occurrence network stability in seawater and microplastic biofilms under prometryn pollution in marine ecosystems. MARINE POLLUTION BULLETIN 2024; 199:115960. [PMID: 38159383 DOI: 10.1016/j.marpolbul.2023.115960] [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: 10/06/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Prometryn has been extensively detected in marine environment because of its widespread usage in agriculture and aquaculture and has been concerns since its serious effects on aquatic organisms. However, its impact on the microbial community in the marine ecosystem including seawater and biofilm is still unclear. Therefore, a short-term indoor microcosm experiment of prometryn exposure was conducted. This study found that prometryn had a more significant impact on the structure and stability of the microbial community in seawater compared to microplastic biofilms. Additionally, we observed that the assembly of the microbial community in biofilms was more affected by stochastic processes than in seawater under the exposure of prometryn. Our study provided evidence for the increasing impact of the microbial communities under the stress of prometryn and microplastics.
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Affiliation(s)
- Mengyao Yang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Lingchao Zhao
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Xiaowen Yu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Wangxinze Shu
- Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Furong Cao
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Qian Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Mingjian Liu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Jun Wang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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Wang X, Zhang G, Ding A, Xie E, Tan Q, Xing Y, Wu H, Tian Q, Zhang Y, Zheng L. Distinctive species interaction patterns under high nitrite stress shape inefficient denitrifying phosphorus removal performance. BIORESOURCE TECHNOLOGY 2024; 394:130269. [PMID: 38154736 DOI: 10.1016/j.biortech.2023.130269] [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: 11/01/2023] [Revised: 12/21/2023] [Accepted: 12/25/2023] [Indexed: 12/30/2023]
Abstract
Denitrifying phosphorus removal using nitrite as an electron acceptor is an innovative, resource-efficient approach for nitrogen and phosphorus removal. However, the inhibitory effects of nitrite on anoxic phosphorus uptake and process stability are unclear. This study investigated the total phosphorus removal performance under nitrite stress and analyzed microbiome responses in 186 sludge samples. The results indicated that the total phosphorus removal rates and dominant taxon abundance were highly similar under nitrite stress. High nitrite stress induced a community-state shift, leading to unstable dynamics and decreased total phosphorus removal. This shift resulted from increased species cooperation. Notably, the shared genera OLB8 and Zoogloea under non-inhibitory nitrite stress, suggesting their vital roles in mitigating nitrite stress by enhancing carbon and energy metabolism. The response patterns of these bacterial communities to high nitrite stress can guide the design and optimization of high-nitrogen wastewater reactors.
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Affiliation(s)
- Xue Wang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Guoyu Zhang
- Department of Environmental Engineering, School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China
| | - Aizhong Ding
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - En Xie
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Qiuyang Tan
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Yuzi Xing
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Haoming Wu
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Qi Tian
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Yaoxin Zhang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Lei Zheng
- College of Water Sciences, Beijing Normal University, Beijing 100875, China.
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Fremin BJ, Bhatt AS, Kyrpides NC. Identification of over ten thousand candidate structured RNAs in viruses and phages. Comput Struct Biotechnol J 2023; 21:5630-5639. [PMID: 38047235 PMCID: PMC10690425 DOI: 10.1016/j.csbj.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 12/05/2023] Open
Abstract
Structured RNAs play crucial roles in viruses, exerting influence over both viral and host gene expression. However, the extensive diversity of structured RNAs and their ability to act in cis or trans positions pose challenges for predicting and assigning their functions. While comparative genomics approaches have successfully predicted candidate structured RNAs in microbes on a large scale, similar efforts for viruses have been lacking. In this study, we screened over 5 million DNA and RNA viral sequences, resulting in the prediction of 10,006 novel candidate structured RNAs. These predictions are widely distributed across taxonomy and ecosystem. We found transcriptional evidence for 206 of these candidate structured RNAs in the human fecal microbiome. These candidate RNAs exhibited evidence of nucleotide covariation, indicative of selective pressure maintaining the predicted secondary structures. Our analysis revealed a diverse repertoire of candidate structured RNAs, encompassing a substantial number of putative tRNAs or tRNA-like structures, Rho-independent transcription terminators, and potentially cis-regulatory structures consistently positioned upstream of genes. In summary, our findings shed light on the extensive diversity of structured RNAs in viruses, offering a valuable resource for further investigations into their functional roles and implications in viral gene expression and pave the way for a deeper understanding of the intricate interplay between viruses and their hosts at the molecular level.
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Affiliation(s)
- Brayon J. Fremin
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ami S. Bhatt
- Blood and Marrow Transplantation) and Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Hematology, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Lead Contact, USA
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Wang L, Lian C, Wan W, Qiu Z, Luo X, Huang Q, Deng Y, Zhang T, Yu K. Salinity-triggered homogeneous selection constrains the microbial function and stability in lakes. Appl Microbiol Biotechnol 2023; 107:6591-6605. [PMID: 37688597 DOI: 10.1007/s00253-023-12696-w] [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: 01/13/2023] [Revised: 05/24/2023] [Accepted: 07/18/2023] [Indexed: 09/11/2023]
Abstract
Climate change and anthropogenic exploitation have led to the gradual salinization of inland waters worldwide. However, the impacts of this process on the prokaryotic plankton communities and their role in biogeochemical cycles in the inland lake are poorly known. Here, we take a space-for-time substitution approach, using 16S rRNA gene amplicon sequencing and metagenomic sequencing. We analyzed the prokaryotic plankton communities of 11 lakes in northwest China, with average water salinities ranging from 0.002 to 14.370%. The results demonstrated that, among the various environmental parameters, salinity was the most important driver of prokaryotic plankton β-diversity (Mantel test, r = 0.53, P < 0.001). (1) Under low salinity, prokaryotic planktons were assembled by stochastic processes and employed diverse halotolerant strategies, including the synthesis and uptake of compatible solutes and extrusion of Na+ or Li+ in exchange for H+. Under elevated salinity pressure, strong homogeneous selection meant that only planktonic prokaryotes showing an energetically favorable halotolerant strategy employing an Mnh-type Na+/H+ antiporter remained. (2) The decreasing taxonomic diversity caused by intense environmental filtering in high-salinity lakes impaired functional diversity related to substance metabolism. The prokaryotes enhanced the TCA cycle, carbon fixation, and low-energy-consumption amino acid biosynthesis in high-salinity lakes. (3) Elevated salinity pressure decreased the negative:positive cohesion and the modularity of the molecular ecology networks for the planktonic prokaryotes, indicating a precarious microbial network. Our findings provide new insights into plankton ecology and are helpful for the protecting of the biodiversity and function of inland lakes against the background of salinization. KEY POINTS: • Increased salinity enhances homogeneous selection in the microbial assembly. • Elevated salinity decreases the microbial co-occurrence networks stability. • High salinity damages the microbial function diversity.
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Affiliation(s)
- Li Wang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Chunang Lian
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Zhiguang Qiu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of ·Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of ·Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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7
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Coclet C, Sorensen PO, Karaoz U, Wang S, Brodie EL, Eloe-Fadrosh EA, Roux S. Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem. MICROBIOME 2023; 11:237. [PMID: 37891627 PMCID: PMC10604447 DOI: 10.1186/s40168-023-01666-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/07/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics' seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. RESULTS We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages (Leviviricetes), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a "seed-bank" viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: "Kill-The-Winner" which proposes that lytic phages are actively infecting abundant bacteria, and "Piggyback-The-Persistent" which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth. CONCLUSION Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry. Video Abstract.
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Affiliation(s)
- Clement Coclet
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Patrick O Sorensen
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shi Wang
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Nonthijun P, Mills N, Mills N, Yongsawas R, Sansupa C, Suwannarach N, Jaikang C, Motanated K, Chayapakdee P, Jongjitngam S, Noirungsee N, Disayathanoowat T. Seasonal Variations in Fungal Communities on the Surfaces of Lan Na Sandstone Sculptures and Their Biodeterioration Capacities. J Fungi (Basel) 2023; 9:833. [PMID: 37623604 PMCID: PMC10455195 DOI: 10.3390/jof9080833] [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: 06/13/2023] [Revised: 08/02/2023] [Accepted: 08/06/2023] [Indexed: 08/26/2023] Open
Abstract
Environmental factors and climate are the primary factors influencing the microbial colonization and deterioration of cultural heritage in outdoor environments. Hence, it is imperative to investigate seasonal variations in microbial communities and the biodeterioration they cause. This study investigated the surfaces of sandstone sculptures at Wat Umong Suan Phutthatham, Chiang Mai, Thailand, during wet and dry seasons using culture-dependent and culture-independent approaches. The fungi isolated from the sandstone sculptures were assessed for biodeterioration attributes including drought tolerance, acid production, calcium crystal formation, and calcium precipitation. The results show that most of the fungal isolates exhibited significant potential for biodeterioration activities. Furthermore, a culture-independent approach was employed to investigate the fungal communities and assess their diversity, interrelationship, and predicted function. The fungal diversity and the communities varied seasonally. The functional prediction indicated that pathotroph-saprotroph fungi comprised the main fungal guild in the dry season, and pathotroph-saprotroph-symbiotroph fungi comprised the dominant guild in the wet season. Remarkably, a network analysis revealed numerous positive correlations among fungal taxa within each season, suggesting a potential synergy that promotes the biodeterioration of sandstone. These findings offer valuable insights into seasonal variations in fungal communities and their impacts on the biodeterioration of sandstone sculptures. This information can be utilized for monitoring, management, and maintenance strategies aimed at preserving this valuable cultural heritage.
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Affiliation(s)
- Paradha Nonthijun
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (P.N.); (N.M.); (N.M.); (R.Y.); (C.S.); (N.S.); (P.C.)
| | - Natasha Mills
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (P.N.); (N.M.); (N.M.); (R.Y.); (C.S.); (N.S.); (P.C.)
| | - Nantana Mills
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (P.N.); (N.M.); (N.M.); (R.Y.); (C.S.); (N.S.); (P.C.)
| | - Rujipas Yongsawas
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (P.N.); (N.M.); (N.M.); (R.Y.); (C.S.); (N.S.); (P.C.)
| | - Chakriya Sansupa
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (P.N.); (N.M.); (N.M.); (R.Y.); (C.S.); (N.S.); (P.C.)
| | - Nakarin Suwannarach
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (P.N.); (N.M.); (N.M.); (R.Y.); (C.S.); (N.S.); (P.C.)
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Churdsak Jaikang
- Toxicology Section, Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Kannipa Motanated
- Department of Geological Sciences, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Pattarasuda Chayapakdee
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (P.N.); (N.M.); (N.M.); (R.Y.); (C.S.); (N.S.); (P.C.)
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Surachai Jongjitngam
- Department of Thai Art, Faculty of Fine Arts, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Nuttapol Noirungsee
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (P.N.); (N.M.); (N.M.); (R.Y.); (C.S.); (N.S.); (P.C.)
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Terd Disayathanoowat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (P.N.); (N.M.); (N.M.); (R.Y.); (C.S.); (N.S.); (P.C.)
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
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Labouyrie M, Ballabio C, Romero F, Panagos P, Jones A, Schmid MW, Mikryukov V, Dulya O, Tedersoo L, Bahram M, Lugato E, van der Heijden MGA, Orgiazzi A. Patterns in soil microbial diversity across Europe. Nat Commun 2023; 14:3311. [PMID: 37291086 PMCID: PMC10250377 DOI: 10.1038/s41467-023-37937-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 04/06/2023] [Indexed: 06/10/2023] Open
Abstract
Factors driving microbial community composition and diversity are well established but the relationship with microbial functioning is poorly understood, especially at large scales. We analysed microbial biodiversity metrics and distribution of potential functional groups along a gradient of increasing land-use perturbation, detecting over 79,000 bacterial and 25,000 fungal OTUs in 715 sites across 24 European countries. We found the lowest bacterial and fungal diversity in less-disturbed environments (woodlands) compared to grasslands and highly-disturbed environments (croplands). Highly-disturbed environments contain significantly more bacterial chemoheterotrophs, harbour a higher proportion of fungal plant pathogens and saprotrophs, and have less beneficial fungal plant symbionts compared to woodlands and extensively-managed grasslands. Spatial patterns of microbial communities and predicted functions are best explained when interactions among the major determinants (vegetation cover, climate, soil properties) are considered. We propose guidelines for environmental policy actions and argue that taxonomical and functional diversity should be considered simultaneously for monitoring purposes.
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Affiliation(s)
- Maëva Labouyrie
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland
| | | | - Ferran Romero
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland
| | - Panos Panagos
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | - Arwyn Jones
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | | | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Olesya Dulya
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Mohammad Bahram
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emanuele Lugato
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | - Marcel G A van der Heijden
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland.
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland.
| | - Alberto Orgiazzi
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy.
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Baldrian P, López-Mondéjar R, Kohout P. Forest microbiome and global change. Nat Rev Microbiol 2023:10.1038/s41579-023-00876-4. [PMID: 36941408 DOI: 10.1038/s41579-023-00876-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 03/23/2023]
Abstract
Forests influence climate and mitigate global change through the storage of carbon in soils. In turn, these complex ecosystems face important challenges, including increases in carbon dioxide, warming, drought and fire, pest outbreaks and nitrogen deposition. The response of forests to these changes is largely mediated by microorganisms, especially fungi and bacteria. The effects of global change differ among boreal, temperate and tropical forests. The future of forests depends mostly on the performance and balance of fungal symbiotic guilds, saprotrophic fungi and bacteria, and fungal plant pathogens. Drought severely weakens forest resilience, as it triggers adverse processes such as pathogen outbreaks and fires that impact the microbial and forest performance for carbon storage and nutrient turnover. Nitrogen deposition also substantially affects forest microbial processes, with a pronounced effect in the temperate zone. Considering plant-microorganism interactions would help predict the future of forests and identify management strategies to increase ecosystem stability and alleviate climate change effects. In this Review, we describe the impact of global change on the forest ecosystem and its microbiome across different climatic zones. We propose potential approaches to control the adverse effects of global change on forest stability, and present future research directions to understand the changes ahead.
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Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Soil and Water Conservation and Waste Management, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
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11
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Roux S, Fischer MG, Hackl T, Katz LA, Schulz F, Yutin N. Updated Virophage Taxonomy and Distinction from Polinton-like Viruses. Biomolecules 2023; 13:204. [PMID: 36830574 PMCID: PMC9952930 DOI: 10.3390/biom13020204] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of "hyperparasitism" in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and taxonomy of this group of viruses. Specifically, virophages have been linked in the literature to other "virophage-like" mobile genetic elements and viruses, including polinton-like viruses (PLVs), but there are no formal demarcation criteria and proper nomenclature for either group, i.e., virophage or PLVs. Here, as part of the ICTV Virophage Study Group, we leverage a large set of genomes gathered from published datasets as well as newly generated protist genomes to propose delineation criteria and classification methods at multiple taxonomic ranks for virophages 'sensu stricto', i.e., genomes related to the prototype isolates Sputnik and mavirus. Based on a combination of comparative genomics and phylogenetic analyses, we show that this group of virophages forms a cohesive taxon that we propose to establish at the class level and suggest a subdivision into four orders and seven families with distinctive ecogenomic features. Finally, to illustrate how the proposed delineation criteria and classification method would be used, we apply these to two recently published datasets, which we show include both virophages and other virophage-related elements. Overall, we see this proposed classification as a necessary first step to provide a robust taxonomic framework in this area of the virosphere, which will need to be expanded in the future to cover other virophage-related viruses such as PLVs.
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Affiliation(s)
- Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthias G. Fischer
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, 69120 Heidelberg, Germany
| | - Thomas Hackl
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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12
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Shao P, Chen Y, Gu D, Zeng J, Zhang S, Wu Y, Lin X. Resistance and resilience of soil bacterial community to zero-valent iron disposal of lindane contamination. CHEMOSPHERE 2022; 306:135612. [PMID: 35817188 DOI: 10.1016/j.chemosphere.2022.135612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/29/2022] [Accepted: 07/03/2022] [Indexed: 06/15/2023]
Abstract
Zero-valent iron (ZVI, Fe0) enables chemical reduction of environmental pollutants coupled with reactivity loss due to surface oxidation. During ZVI treatment process, however, microbial community stability in terms of resistance and resilience remains largely unclear. Here, we monitored bacterial community succession over a 4 weeks period in soil microcosms with or without 2% (w/w) Fe0 amendment. To simulate soil pollution, 100 μg g-1 chlorinated pesticide lindane (γ-hexachlorocyclohexane) was added to the microcosms as a model contaminant. In addition to microbial activity as measured by soil organic carbon mineralization, bacterial abundance, diversity and composition were determined using qPCR and high-throughput sequencing of 16 S rRNA genes. Co-occurrence analysis was performed to reveal the interaction patterns within the bacterial communities. The results indicated that ZVI caused near-complete transformation of lindane, while in the microcosms without Fe0 amendment the pesticide was recalcitrant. ZVI strongly inhibited CO2-efflux at the early stage of incubation, but the bacterial community appeared to be less sensitive to Fe0 amendment. The ratios of negative to positive correlations between network nodes suggested that Fe0 had marginal influence on community stability compared to the lindane treatments, which destabilized the bacterial community. Community succession occurred in the presence of ZVI, as exemplified by a dominancy transition from anaerobic to aerobic taxa. Yet, ZVI alleviated the stress of lindane on soil bacteria by improving community structure and increasing network complexity. Taken together, these findings demonstrate the stability of soil bacterial community under Fe0 stress, which might be conducive to functional recovery of soil microorganisms following ZVI remediation.
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Affiliation(s)
- Pengfei Shao
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China.
| | - Yuzhu Chen
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China
| | - Decheng Gu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China
| | - Jun Zeng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China
| | - Shimin Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Yucheng Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China.
| | - Xiangui Lin
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China
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13
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Beier S, Werner J, Bouvier T, Mouquet N, Violle C. Trait-trait relationships and tradeoffs vary with genome size in prokaryotes. Front Microbiol 2022; 13:985216. [PMID: 36338105 PMCID: PMC9634001 DOI: 10.3389/fmicb.2022.985216] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
We report genomic traits that have been associated with the life history of prokaryotes and highlight conflicting findings concerning earlier observed trait correlations and tradeoffs. In order to address possible explanations for these contradictions we examined trait–trait variations of 11 genomic traits from ~18,000 sequenced genomes. The studied trait–trait variations suggested: (i) the predominance of two resistance and resilience-related orthogonal axes and (ii) at least in free living species with large effective population sizes whose evolution is little affected by genetic drift an overlap between a resilience axis and an oligotrophic-copiotrophic axis. These findings imply that resistance associated traits of prokaryotes are globally decoupled from resilience related traits and in the case of free-living communities also from traits associated with resource availability. However, further inspection of pairwise scatterplots showed that resistance and resilience traits tended to be positively related for genomes up to roughly five million base pairs and negatively for larger genomes. Genome size distributions differ across habitats and our findings therefore point to habitat dependent tradeoffs between resistance and resilience. This in turn may preclude a globally consistent assignment of prokaryote genomic traits to the competitor - stress-tolerator - ruderal (CSR) schema that sorts species depending on their location along disturbance and productivity gradients into three ecological strategies and may serve as an explanation for conflicting findings from earlier studies. All reviewed genomic traits featured significant phylogenetic signals and we propose that our trait table can be applied to extrapolate genomic traits from taxonomic marker genes. This will enable to empirically evaluate the assembly of these genomic traits in prokaryotic communities from different habitats and under different productivity and disturbance scenarios as predicted via the resistance-resilience framework formulated here.
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Affiliation(s)
- Sara Beier
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Germany
- UMR 7621 Laboratoire d’Océanographie Microbienne, Observatoire Océanologique de Banyuls-sur-Mer, Sorbonne Université, Banyuls-sur-Mer, France
- *Correspondence: Sara Beier,
| | - Johannes Werner
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Germany
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Thierry Bouvier
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Nicolas Mouquet
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Centre for the Synthesis and Analysis of Biodiversity, Montpellier, France
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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14
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Thousands of small, novel genes predicted in global phage genomes. Cell Rep 2022; 39:110984. [PMID: 35732113 DOI: 10.1016/j.celrep.2022.110984] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/14/2022] [Accepted: 05/27/2022] [Indexed: 11/22/2022] Open
Abstract
Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.
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15
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Corona Ramírez A, Cailleau G, Fatton M, Dorador C, Junier P. Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco. Front Microbiol 2022; 13:826117. [PMID: 36687602 PMCID: PMC9847572 DOI: 10.3389/fmicb.2022.826117] [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: 11/30/2021] [Accepted: 03/07/2022] [Indexed: 01/25/2023] Open
Abstract
The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores under suboptimal growth conditions (e.g., starvation). In contrast, little is known about the production of specialized resting cells in archaea. In this study, we applied a culture-independent method that uses physical and chemical lysis, to assess the diversity of lysis-resistant bacteria and archaea and compare it to the overall prokaryotic diversity (direct DNA extraction). The diversity of lysis-resistant cells was studied in the polyextreme environment of the Salar de Huasco. The Salar de Huasco is a high-altitude athalassohaline wetland in the Chilean Altiplano. Previous studies have shown a high diversity of bacteria and archaea in the Salar de Huasco, but the diversity of lysis-resistant microorganisms has never been investigated. The underlying hypothesis was that the combination of extreme abiotic conditions might favor the production of specialized resting cells. Samples were collected from sediment cores along a saline gradient and microbial mats were collected in small surrounding ponds. A significantly different diversity and composition were found in the sediment cores or microbial mats. Furthermore, our results show a high diversity of lysis-resistant cells not only in bacteria but also in archaea. The bacterial lysis-resistant fraction was distinct in comparison to the overall community. Also, the ability to survive the lysis-resistant treatment was restricted to a few groups, including known spore-forming phyla such as Firmicutes and Actinobacteria. In contrast to bacteria, lysis resistance was widely spread in archaea, hinting at a generalized resistance to lysis, which is at least comparable to the resistance of dormant cells in bacteria. The enrichment of Natrinema and Halarchaeum in the lysis-resistant fraction could hint at the production of cyst-like cells or other resistant cells. These results can guide future studies aiming to isolate and broaden the characterization of lysis-resistant archaea.
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Affiliation(s)
- Andrea Corona Ramírez
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Mathilda Fatton
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Cristina Dorador
- Department of Biotechnology, University of Antofagasta, Antofagasta, Chile
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland,*Correspondence: Pilar Junier,
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16
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Zhang Y, Zhang Y, Xu W, Hu J, Zhang Z. Possible effects of temperature on bacterial communities in the rhizosphere of rice under different climatic regions. Arch Microbiol 2022; 204:212. [PMID: 35296917 DOI: 10.1007/s00203-022-02812-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/21/2022] [Accepted: 02/18/2022] [Indexed: 11/25/2022]
Abstract
Global warming is an indisputable fact. However, the effect of warming on the rhizosphere bacterial community of crops is not well understood. Therefore, we carried out pot experiments with three rice (Oryza sativa L.) varieties in black soil across three climatic regions of northeast China to simulate temperature change, and analyzed the response of the rhizosphere bacterial community to different temperatures. Results showed that climate had stronger effects on rhizosphere bacterial communities than rice variety. The rhizosphere bacterial diversity differed significantly among the three climatic regions and positively correlated with the mean daily average temperature (MAveT), mean daily maximum temperature (MMaxT), and mean daily minimum temperature (MMinT), and negatively correlated with the daily temperature range (DTR). Principal co-ordinate analysis revealed that bulk soil bacterial communities maintained a high similarity across the three climatic regions, while rhizosphere bacterial communities notably varied. This change was significantly correlated with MAveT, MMaxT, MMinT, and DTR. Compared with bulk soil, Proteobacteria and Bacteroidetes were enriched in the rhizosphere, while Actinobacteria was depleted. Moreover, these changes were strengthened by increasing the temperature and decreasing DTR. Additionally, correlation analysis revealed that changes in rhizosphere bacterial communities were closely related to the formation of rice yields. Our study revealed that the increasing temperature indirectly reshapes the rhizosphere bacterial community that may promote rice production in areas with lower temperatures.
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Affiliation(s)
- Yang Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China
| | - Yujie Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China
| | - Wenjie Xu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China
| | - Jian Hu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China.
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, People's Republic of China.
| | - Zujian Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China.
- Innovation Center of Rice Cultivation Technology in Yangtze Valley, Ministry of Agriculture/Key Laboratory of Crop Genetic and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, 225009, People's Republic of China.
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17
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Burnett MS, Schütte UM, Harms TK. WIDESPREAD CAPACITY FOR DENITRIFICATION ACROSS A BOREAL FOREST LANDSCAPE. BIOGEOCHEMISTRY 2022; 158:215-232. [PMID: 36186670 PMCID: PMC9518932 DOI: 10.1007/s10533-022-00895-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/18/2022] [Indexed: 06/16/2023]
Abstract
A warming climate combined with frequent and severe fires cause permafrost to thaw, especially in the region of discontinuous permafrost, where soil temperatures may only be a few degrees below 0 °C. Soil thaw releases carbon (C) and nitrogen (N) into the actively cycling pools, and whereas C emissions following permafrost thaw are well documented, the fates of N remain unclear. Denitrification could release N from ecosystems as nitrous oxide (N2O) or nitrogen gas (N2), but the contributions of these processes to the high-latitude N cycle remain uncertain. We quantified microbial capacity for denitrification and N2O production in boreal soils, lakes, and streams using anoxic C- and N-amended assays, and assessed correlates of denitrifying enzyme activity (DEA) in Interior Alaska. Riparian soils and stream sediments supported the highest potential rates of denitrification, upland soils were intermediate, and lakes supported lower rates, whereas deep permafrost soils supported little denitrification. Time since fire had no effect on denitrification potential in upland soils. Across all landscape positions, DEA was negatively correlated with ammonium pools. Within each landscape position, potential rate of denitrification increased with soil or sediment organic matter content. Widespread N loss to denitrification in boreal forests could constrain the capacity for N-limited primary producers to maintain C stocks in soils following permafrost thaw.
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Affiliation(s)
- Melanie S. Burnett
- Institute of Arctic Biology and Department of Biology & Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
- Department of Earth and Planetary Science, McGill University, Montréal, Quebec H3A 2A7, Canada
| | - Ursel M.E. Schütte
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
| | - Tamara K. Harms
- Institute of Arctic Biology and Department of Biology & Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
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18
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Kaufmann C, Cassin-Sackett L. Fine-Scale Spatial Structure of Soil Microbial Communities in Burrows of a Keystone Rodent Following Mass Mortality. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.758348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Soil microbial communities both reflect and influence biotic and abiotic processes occurring at or near the soil surface. Ecosystem engineers that physically alter the soil surface, such as burrowing ground squirrels, are expected to influence the distribution of soil microbial communities. Black-tailed prairie dogs (Cynomys ludovicianus) construct complex burrows in which activities such as nesting, defecating, and dying are partitioned spatially into different chambers. Prairie dogs also experience large-scale die-offs due to sylvatic plague, caused by the bacterium Yersinia pestis, which lead to mass mortality events with potential repercussions on microbial communities. We used 16S sequencing to examine microbial communities in soil that was excavated by prairie dogs from different burrow locations, and surface soil that was used in the construction of burrow entrances, in populations that experienced plague die-offs. Following the QIIME2 pipeline, we assessed microbial diversity at several taxonomic levels among burrow regions. To do so, we computed community similarity metrics (Bray–Curtis, Jaccard, and weighted and unweighted UniFrac) among samples and community diversity indexes (Shannon and Faith phylogenetic diversity indexes) within each sample. Microbial communities differed across burrow regions, and several taxa exhibited spatial variation in relative abundance. Microbial ecological diversity (Shannon index) was highest in soil recently excavated from within burrows and soils associated with dead animals, and was lowest in soils associated with scat. Phylogenetic diversity varied only marginally within burrows, but the trends paralleled those for Shannon diversity. Yersinia was detected in four samples from one colony, marking the first time the genus has been sampled from soil on prairie dog colonies. The presence of Yersinia was a significant predictor of five bacterial families and eight microbial genera, most of which were rare taxa found in higher abundance in the presence of Yersinia, and one of which, Dictyostelium, has been proposed as an enzootic reservoir of Y. pestis. This study demonstrates that mammalian modifications to soil structure by physical alterations and by mass mortality can influence the distribution and diversity of microbial communities.
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19
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Hernandez DJ, David AS, Menges ES, Searcy CA, Afkhami ME. Environmental stress destabilizes microbial networks. THE ISME JOURNAL 2021; 15:1722-1734. [PMID: 33452480 PMCID: PMC8163744 DOI: 10.1038/s41396-020-00882-x] [Citation(s) in RCA: 366] [Impact Index Per Article: 122.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 01/29/2023]
Abstract
Environmental stress is increasing worldwide, yet we lack a clear picture of how stress disrupts the stability of microbial communities and the ecosystem services they provide. Here, we present the first evidence that naturally-occurring microbiomes display network properties characteristic of unstable communities when under persistent stress. By assessing changes in diversity and structure of soil microbiomes along 40 replicate stress gradients (elevation/water availability gradients) in the Florida scrub ecosystem, we show that: (1) prokaryotic and fungal diversity decline in high stress, and (2) two network properties of stable microbial communities-modularity and negative:positive cohesion-have a clear negative relationship with environmental stress, explaining 51-78% of their variation. Interestingly, pathogenic taxa/functional guilds decreased in relative abundance along the stress gradient, while oligotrophs and mutualists increased, suggesting that the shift in negative:positive cohesion could result from decreasing negative:positive biotic interactions consistent with the predictions of the Stress Gradient Hypothesis. Given the crucial role microbiomes play in ecosystem functions, our results suggest that, by limiting the compartmentalization of microbial associations and creating communities dominated by positive associations, increasing stress in the Anthropocene could destabilize microbiomes and undermine their ecosystem services.
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Affiliation(s)
- Damian J. Hernandez
- grid.26790.3a0000 0004 1936 8606Department of Biology, University of Miami, Coral Gables, FL 33146 USA
| | - Aaron S. David
- grid.26790.3a0000 0004 1936 8606Department of Biology, University of Miami, Coral Gables, FL 33146 USA ,grid.508985.9USDA-ARS, Invasive Plant Research Laboratory, Fort Lauderdale, FL 33314 USA
| | - Eric S. Menges
- grid.248717.f0000 0000 9407 7092Archbold Biological Station, Venus, FL 33960 USA
| | - Christopher A. Searcy
- grid.26790.3a0000 0004 1936 8606Department of Biology, University of Miami, Coral Gables, FL 33146 USA
| | - Michelle E. Afkhami
- grid.26790.3a0000 0004 1936 8606Department of Biology, University of Miami, Coral Gables, FL 33146 USA
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20
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Alster CJ, Allison SD, Glassman SI, Martiny AC, Treseder KK. Exploring Trait Trade-Offs for Fungal Decomposers in a Southern California Grassland. Front Microbiol 2021; 12:655987. [PMID: 33995318 PMCID: PMC8118720 DOI: 10.3389/fmicb.2021.655987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 11/14/2022] Open
Abstract
Fungi are important decomposers in terrestrial ecosystems, so their responses to climate change might influence carbon (C) and nitrogen (N) dynamics. We investigated whether growth and activity of fungi under drought conditions were structured by trade-offs among traits in 15 fungal isolates from a Mediterranean Southern California grassland. We inoculated fungi onto sterilized litter that was incubated at three moisture levels (4, 27, and 50% water holding capacity, WHC). For each isolate, we characterized traits that described three potential lifestyles within the newly proposed “YAS” framework: growth yield, resource acquisition, and stress tolerance. Specifically, we measured fungal hyphal length per unit litter decomposition for growth yield; the potential activities of the extracellular enzymes cellobiohydrolase (CBH), β-glucosidase (BG), β-xylosidase (BX), and N-acetyl-β-D-glucosaminidase (NAG) for resource acquisition; and ability to grow in drought vs. higher moisture levels for drought stress tolerance. Although, we had hypothesized that evolutionary and physiological trade-offs would elicit negative relationships among traits, we found no supporting evidence for this hypothesis. Across isolates, growth yield, drought stress tolerance, and extracellular enzyme activities were not significantly related to each other. Thus, it is possible that drought-induced shifts in fungal community composition may not necessarily lead to changes in fungal biomass or decomposer ability in this arid grassland.
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Affiliation(s)
- Charlotte J Alster
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
| | - Steven D Allison
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States.,Department of Earth System Science, University of California Irvine, Irvine, CA, United States
| | - Sydney I Glassman
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States
| | - Adam C Martiny
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States.,Department of Earth System Science, University of California Irvine, Irvine, CA, United States
| | - Kathleen K Treseder
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
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