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Tomazelli D, Klauberg-Filho O, Mendes LW, Goss-Souza D. The impact of land-use changes and management intensification on bacterial communities in the last decade: a review. Appl Environ Microbiol 2024; 90:e0030924. [PMID: 38874336 PMCID: PMC11267915 DOI: 10.1128/aem.00309-24] [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] [Indexed: 06/15/2024] Open
Abstract
In the last decade, advances in soil bacterial ecology have contributed to increasing agricultural production. Brazil is the world leading agriculture producer and leading soil biodiversity reservoir. Meanwhile, there is still a significant gap in the knowledge regarding the soil microscopic life and its interactions with agricultural practices, and the replacement of natural vegetation by agroecosystems is yet to be unfolded. Through high throughput DNA sequencing, scientists are now exploring the complexity of soil bacterial communities and their relationship with soil and environmental characteristics. This study aimed to investigate the progress of bacterial ecology studies in Brazil over the last 10 years, seeking to understand the effect of the conversion of natural vegetation in agricultural systems on the diversity and structure of the soil microbial communities. We conducted a systematic search for scientific publication databases. Our systematic search has matched 62 scientific articles from three different databases. Most of the studies were placed in southeastern and northern Brazil, with no records of studies about microbial ecology in 17 out of 27 Brazilian states. Out of the 26 studies that examined the effects of replacing natural vegetation with agroecosystems, most authors concluded that changes in soil pH and vegetation cover replacement were the primary drivers of shifts in microbial communities. Understanding the ecology of the bacteria inhabiting Brazilian soils in agroecosystems is paramount for developing more efficient soil management strategies and cleaner agricultural technologies.
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Affiliation(s)
- Daniela Tomazelli
- Department of Soils and Natural Resources, Santa Catarina State University, Lages, Santa Catarina, Brazil
| | - Osmar Klauberg-Filho
- Department of Soils and Natural Resources, Santa Catarina State University, Lages, Santa Catarina, Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Dennis Goss-Souza
- College of Agronomy, Federal Institute of Paraná, Palmas, Paraná, Brazil
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2
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Bereczki K, Tóth EG, Szili-Kovács T, Megyes M, Korponai K, Lados BB, Illés G, Benke A, Márialigeti K. Soil Parameters and Forest Structure Commonly Form the Microbiome Composition and Activity of Topsoil Layers in Planted Forests. Microorganisms 2024; 12:1162. [PMID: 38930544 PMCID: PMC11205539 DOI: 10.3390/microorganisms12061162] [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: 05/10/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Soil bacterial communities play a remarkable role in nutrient cycling, significantly affecting soil organic material content, soil fertility, and, in an indirect way, plant succession processes. Conversely, vegetation type influences microbial soil life. The present study compared the bacterial microbiome composition, diversity and catabolic activity profile of topsoil samples collected under three different forest types (a twice-coppiced black locust stand, a young, naturally reforested, and a middle-aged mixed pedunculate oak stand) planted on former arable land in the early 20th century. Diversity indices determined during 16S ribosomal RNA sequencing-based metagenome analysis indicated that the black locust stand had the highest soil bacterial community diversity. At the phylum level, Acidobacteriota, Actinobacteriota, Proteobacteria, Verrucomicrobiota, Bacteroidota, and Gemmatimonadota were the most abundant taxa in the forest soils. Concerning soil parameters, redundancy analysis revealed that pH had the highest impact on bacterial community structure and pH, and soil organic carbon content on the samples' respiration patterns. As for catabolic activity, the recently clearcut oak forest showed the lowest substrate-induced respiration, and citrate was the main driver for the inter-stand variability of microbial activity. Our results confirm that soil parameters and forest type influence the composition and functioning of the soil bacterial microbiome.
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Affiliation(s)
- Katalin Bereczki
- Doctoral School of Environmental Sciences, Eötvös Loránd University, 1117 Budapest, Hungary;
- Department of Forest Management and Ecology, Forest Research Institute, University of Sopron, 9600 Sárvár, Hungary;
| | - Endre György Tóth
- National Coalition of Independent Scholars (NCIS), Brattleboro, VT 05301, USA;
| | - Tibor Szili-Kovács
- Institute for Soil Sciences, Centre for Agricultural Research, 1022 Budapest, Hungary;
| | - Melinda Megyes
- Doctoral School of Environmental Sciences, Eötvös Loránd University, 1117 Budapest, Hungary;
| | - Kristóf Korponai
- Department of Plant Molecular Biology, Agricultural Institute, Centre for Agricultural Research, 2462 Martonvásár, Hungary;
| | - Botond Boldizsár Lados
- Department of Forestry Breeding, Forest Research Institute, University of Sopron, 9600 Sárvár, Hungary; (B.B.L.); (A.B.)
| | - Gábor Illés
- Department of Forest Management and Ecology, Forest Research Institute, University of Sopron, 9600 Sárvár, Hungary;
| | - Attila Benke
- Department of Forestry Breeding, Forest Research Institute, University of Sopron, 9600 Sárvár, Hungary; (B.B.L.); (A.B.)
| | - Károly Márialigeti
- Department of Microbiology, Eötvös Loránd University, 1117 Budapest, Hungary;
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Rolls RJ, Deane DC, Johnson SE, Heino J, Anderson MJ, Ellingsen KE. Biotic homogenisation and differentiation as directional change in beta diversity: synthesising driver-response relationships to develop conceptual models across ecosystems. Biol Rev Camb Philos Soc 2023; 98:1388-1423. [PMID: 37072381 DOI: 10.1111/brv.12958] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/20/2023]
Abstract
Biotic homogenisation is defined as decreasing dissimilarity among ecological assemblages sampled within a given spatial area over time. Biotic differentiation, in turn, is defined as increasing dissimilarity over time. Overall, changes in the spatial dissimilarities among assemblages (termed 'beta diversity') is an increasingly recognised feature of broader biodiversity change in the Anthropocene. Empirical evidence of biotic homogenisation and biotic differentiation remains scattered across different ecosystems. Most meta-analyses quantify the prevalence and direction of change in beta diversity, rather than attempting to identify underlying ecological drivers of such changes. By conceptualising the mechanisms that contribute to decreasing or increasing dissimilarity in the composition of ecological assemblages across space, environmental managers and conservation practitioners can make informed decisions about what interventions may be required to sustain biodiversity and can predict potential biodiversity outcomes of future disturbances. We systematically reviewed and synthesised published empirical evidence for ecological drivers of biotic homogenisation and differentiation across terrestrial, marine, and freshwater realms to derive conceptual models that explain changes in spatial beta diversity. We pursued five key themes in our review: (i) temporal environmental change; (ii) disturbance regime; (iii) connectivity alteration and species redistribution; (iv) habitat change; and (v) biotic and trophic interactions. Our first conceptual model highlights how biotic homogenisation and differentiation can occur as a function of changes in local (alpha) diversity or regional (gamma) diversity, independently of species invasions and losses due to changes in species occurrence among assemblages. Second, the direction and magnitude of change in beta diversity depends on the interaction between spatial variation (patchiness) and temporal variation (synchronicity) of disturbance events. Third, in the context of connectivity and species redistribution, divergent beta diversity outcomes occur as different species have different dispersal characteristics, and the magnitude of beta diversity change associated with species invasions also depends strongly on alpha and gamma diversity prior to species invasion. Fourth, beta diversity is positively linked with spatial environmental variability, such that biotic homogenisation and differentiation occur when environmental heterogeneity decreases or increases, respectively. Fifth, species interactions can influence beta diversity via habitat modification, disease, consumption (trophic dynamics), competition, and by altering ecosystem productivity. Our synthesis highlights the multitude of mechanisms that cause assemblages to be more or less spatially similar in composition (taxonomically, functionally, phylogenetically) through time. We consider that future studies should aim to enhance our collective understanding of ecological systems by clarifying the underlying mechanisms driving homogenisation or differentiation, rather than focusing only on reporting the prevalence and direction of change in beta diversity, per se.
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Affiliation(s)
- Robert J Rolls
- School of Environmental and Rural Sciences, University of New England, Armidale, New South Wales, 2351, Australia
| | - David C Deane
- School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Sarah E Johnson
- Natural Resources Department, Northland College, Ashland, WI, 54891, USA
| | - Jani Heino
- Geography Research Unit, University of Oulu, P.O. Box 8000, Oulu, FI-90014, Finland
| | - Marti J Anderson
- New Zealand Institute for Advanced Study (NZIAS), Massey University, Albany Campus, Auckland, New Zealand
| | - Kari E Ellingsen
- Norwegian Institute for Nature Research (NINA), Fram Centre, P.O. Box 6606 Langnes, Tromsø, 9296, Norway
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Obregon Alvarez D, Fonseca de Souza L, Mendes LW, de Moraes MT, Tosi M, Venturini AM, Meyer KM, Barbosa de Camargo P, Bohannan BJM, Mazza Rodrigues JL, Dunfield KE, Tsai SM. Shifts in functional traits and interactions patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin. Mol Ecol 2023. [PMID: 36896778 DOI: 10.1111/mec.16912] [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: 09/15/2022] [Revised: 01/24/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023]
Abstract
Deforestation threatens the integrity of the Amazon biome and the ecosystem services it provides, including greenhouse gas mitigation. Forest-to-pasture conversion has been shown to alter the flux of methane gas (CH4 ) in Amazonian soils, driving a switch from acting as a sink to a source of atmospheric CH4 . This study aimed to better understand this phenomenon by investigating soil microbial metagenomes, focusing on the taxonomic and functional structure of methane-cycling communities. Metagenomic data from forest and pasture soils were combined with measurements of in situ CH4 fluxes and soil edaphic factors and analysed using multivariate statistical approaches. We found a significantly higher abundance and diversity of methanogens in pasture soils. As inferred by co-occurrence networks, these microorganisms seem to be less interconnected within the soil microbiota in pasture soils. Metabolic traits were also different between land uses, with increased hydrogenotrophic and methylotrophic pathways of methanogenesis in pasture soils. Land-use change also induced shifts in taxonomic and functional traits of methanotrophs, with bacteria harbouring genes encoding the soluble form of methane monooxygenase enzyme (sMMO) depleted in pasture soils. Redundancy analysis and multimodel inference revealed that the shift in methane-cycling communities was associated with high pH, organic matter, soil porosity and micronutrients in pasture soils. These results comprehensively characterize the effect of forest-to-pasture conversion on the microbial communities driving the methane-cycling microorganisms in the Amazon rainforest, which will contribute to the efforts to preserve this important biome.
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Affiliation(s)
- Dasiel Obregon Alvarez
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | | | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | | | - Micaela Tosi
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | | | - Kyle M Meyer
- Department of Integrative Biology, University of California-Berkeley, Berkeley, California, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | | | | | - Jorge L Mazza Rodrigues
- Department of Land, Air, and Water Resources, University of California-Davis, Davis, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Siu Mui Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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5
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Comparative Genomics and Physiology of Akkermansia muciniphila Isolates from Human Intestine Reveal Specialized Mucosal Adaptation. Microorganisms 2022; 10:microorganisms10081605. [PMID: 36014023 PMCID: PMC9415379 DOI: 10.3390/microorganisms10081605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/24/2022] [Accepted: 08/07/2022] [Indexed: 01/07/2023] Open
Abstract
Akkermansia muciniphila is a champion of mucin degradation in the human gastrointestinal tract. Here, we report the isolation of six novel strains from healthy human donors and their genomic, proteomic and physiological characterization in comparison to the type-strains A. muciniphila MucT and A. glycaniphila PytT. Complete genome sequencing revealed that, despite their large genomic similarity (>97.6%), the novel isolates clustered into two distinct subspecies of A. muciniphila: Amuc1, which includes the type-strain MucT, and AmucU, a cluster of unassigned strains that have not yet been well characterized. CRISPR analysis showed all strains to be unique and confirmed that single healthy subjects can carry more than one A. muciniphila strain. Mucin degradation pathways were strongly conserved amongst all isolates, illustrating the exemplary niche adaptation of A. muciniphila to the mucin interface. This was confirmed by analysis of the predicted glycoside hydrolase profiles and supported by comparing the proteomes of A. muciniphila strain H2, belonging to the AmucU cluster, to MucT and A. glycaniphila PytT (including 610 and 727 proteins, respectively). While some intrinsic resistance was observed among the A. muciniphila straind, none of these seem to pose strain-specific risks in terms of their antibiotic resistance patterns nor a significant risk for the horizontal transfer of antibiotic resistance determinants, opening the way to apply the type-strain MucT or these new A. muciniphila strains as next generation beneficial microbes.
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Zhang P, Guan P, Hao C, Yang J, Xie Z, Wu D. Changes in assembly processes of soil microbial communities in forest-to-cropland conversion in Changbai Mountains, northeastern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151738. [PMID: 34808170 DOI: 10.1016/j.scitotenv.2021.151738] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 11/05/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
In response to human-induced changes in the environment, it is crucial to assess the underlying factors of the impacts of forest conversion on ecosystem function. However, research is limited on bacteria and fungi diversity, functional properties, and community assembly mechanisms in response to forest-to-cropland conversion. We categorized soil bacterial and fungal communities from primary forest, secondary forest, and cropland in Changbai Mountains, China. We found that forest-to-cropland conversion altered the structure and composition of bacterial and fungal communities and might be associated with potential changes in function. The null models indicated that the conversion from forest to cropland enhanced the bacterial dispersal limitation process and weakened the fungal dispersal limitation processes. Furthermore, ecological drift dominates the ecological processes of cropland fungi. Both edaphic properties (the content of C: N ratio, available phosphorus, nitrate) significantly impacted on soil bacterial and fungal community structures. In addition, there were significant functional variations in the fungal community between forest-to-cropland. The ectomycorrhizal and saprotrophic fungi showed increased abundance in the forest microbial communities, whereas the endophytic and pathogenic fungal abundance was increased in cropland soil. Taken together, our data illustrate the differences in the response of bacteria and fungi to forest-to-cropland conversion in temperate forest areas and deepen our understanding of the effects of forest conversion on microbial functions and community assembly processes.
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Affiliation(s)
- Peng Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pingting Guan
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Cao Hao
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Jingjing Yang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Zhijing Xie
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Donghui Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun 130024, China; Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China.
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Costa DPD, Araujo ASF, Pereira APDA, Mendes LW, França RFD, Silva TDGED, Oliveira JBD, Araujo JS, Duda GP, Menezes RSC, Medeiros EVD. Forest-to-pasture conversion modifies the soil bacterial community in Brazilian dry forest Caatinga. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:151943. [PMID: 34864020 DOI: 10.1016/j.scitotenv.2021.151943] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/21/2021] [Accepted: 11/20/2021] [Indexed: 06/13/2023]
Abstract
Soils comprise a huge fraction of the world's biodiversity, contributing to several crucial ecosystem functions. However, how the forest-to-pasture conversion impact soil bacterial diversity remains poorly understood, mainly in the Caatinga biome, the largest tropical dry forest of the world. Here, we hypothesized that forest-to-pasture conversion would shape the microbial community. Thus, the soil bacterial community was assessed using the 16S rRNA gene sequencing into the Illumina MiSeq platform. Then, we analyzed ecological patterns and correlated the bacterial community with environmental parameters in forest, and two distinct pastures areas, one less productive and another more productive. The variation in soil properties in pastures and forest influenced the structure and diversity of the bacterial community. Thus, the more productive pasture positively influenced the proportion of specialists and the co-occurrence network compared to the less productive pasture. Also, Proteobacteria, Acidobacteria, and Verrucomicrobia were abundant under forest, while Actinobacteria, Firmicutes, and Chloroflexi were abundant under pastures. Also, the more productive pasture presented a higher bacterial diversity, which is important since that a more stable and connected bacterial community could benefit the agricultural environment and enhance plant performance, as can be observed by the highest network complexity in this pasture. Together, our findings elucidate a significant shift in soil bacterial communities as a consequence of forest-to-pasture conversion and bring important information for the development of preservation strategies.
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Affiliation(s)
- Diogo Paes da Costa
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil.
| | | | | | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, 13400-970 Piracicaba, SP, Brazil.
| | - Rafaela Felix da França
- Department of Soils, Federal Rural University of Rio de Janeiro, 23890-000 Seropédica, RJ, Brazil.
| | | | - Julyana Braga de Oliveira
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil.
| | - Jenifer Sthephanie Araujo
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil.
| | - Gustavo Pereira Duda
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil.
| | | | - Erika Valente de Medeiros
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil.
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Khalid M, Du B, Tan H, Liu X, Su L, Ali M, Liu C, Sun N, Hui N. Phosphorus elevation erodes ectomycorrhizal community diversity and induces divergence of saprophytic community composition between vegetation types. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148502. [PMID: 34166904 DOI: 10.1016/j.scitotenv.2021.148502] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/13/2021] [Accepted: 06/13/2021] [Indexed: 06/13/2023]
Abstract
Phosphorus (P) is a critical macronutrient that is essential for many life-sustaining processes. Despite decades of work on plant performance under P deficiency and the importance of microbes in ecosystem processes, little is known about how bacterial and fungal flora respond to P gradients and determine the vegetation health. In current study, we examined soil edaphic conditions and microbial communities in 39 untouched natural forests representing phosphorous deficient (Pp) and phosphorus rich (Pr) soils (due to naturally occurring phosphate rocks) in Yunnan Province, China. We also considered the effect of plant functional types by including the dominant tree species. Bacterial and fungal diversity was greater across the Pp sites compared with Pr sites. The relative abundance of Actinobacteria and Gemmatimonadetes was higher across Pp sites, while Chlamydiae and Verrucomicrobia showed the opposite pattern, with greater relative abundance across the Pr sites. Bacterial taxa that were observed in low P soils were more likely having oligotrophic life history strategies. Interestingly, ectomycorrhizal (ECM) fungal diversity was promoted in the Pp sites, indicating that the decreasing soil P concentration and the increasing host P demand foster stimulated the ECM species for hyphal soil exploration. Moreover, the high P level caused saprophytic fungi (SAP) to diverge, causing its enrichment only under Q. variabilis compared to low P soil, where there is no difference in relative abundance of SAP between the two tree species. This likely resulted in an enhanced decomposition process by SAP and elevation of soil properties (Carbon and Nitrogen) under Q. variabilis across the Pr sites. Taken together, our findings highlight the highly diverse microbiome in low P soils. The higher soil P caused shifts of fungal functional guilds, which likely influence tree growth and health (ECM), along with divergence of ecosystem services between tree functional types.
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Affiliation(s)
- Muhammad Khalid
- Key Laboratory of Urban Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Baoming Du
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haoxin Tan
- Key Laboratory of Urban Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinxin Liu
- Key Laboratory of Urban Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lantian Su
- Key Laboratory of Urban Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mehran Ali
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunjiang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ningxiao Sun
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Nan Hui
- Key Laboratory of Urban Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai 200240, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd., Shanghai 200240, China.
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9
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Hermans SM, Taylor M, Grelet G, Curran-Cournane F, Buckley HL, Handley KM, Lear G. From pine to pasture: land use history has long-term impacts on soil bacterial community composition and functional potential. FEMS Microbiol Ecol 2020; 96:5807072. [PMID: 32175557 DOI: 10.1093/femsec/fiaa041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/09/2020] [Indexed: 11/13/2022] Open
Abstract
Bacterial communities are crucial to soil ecosystems and are known to be sensitive to environmental changes. However, our understanding of how present-day soil bacterial communities remain impacted by historic land uses is limited; implications for their functional potential are especially understudied. Through 16S rRNA gene amplicon and shotgun metagenomic sequencing, we characterized the structure and functional potential of soil bacterial communities after land use conversion. Sites converted from pine plantations to dairy pasture were sampled five- and eight-years post conversion. The bacterial community composition and functional potential at these sites were compared to long-term dairy pastures and pine forest reference sites. Bacterial community composition and functional potential at the converted sites differed significantly from those at reference sites (P = 0.001). On average, they were more similar to those in the long-term dairy sites and showed gradual convergence (P = 0.001). Differences in composition and functional potential were most strongly related to nutrients such as nitrogen, Olsen P and the carbon to nitrogen ratio. Genes related to the cycling of nitrogen, especially denitrification, were underrepresented in converted sites compared to long-term pasture soils. Together, our study highlights the long-lasting impacts land use conversion can have on microbial communities, and the implications for future soil health and functioning.
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Affiliation(s)
- Syrie M Hermans
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, New Zealand
| | - Matthew Taylor
- Waikato Regional Council, 401 Grey Street, Hamilton 3216, New Zealand
| | - Gwen Grelet
- Manaaki Whenua - Landcare Research, 54 Gerald Street, Lincoln, New Zealand
| | - Fiona Curran-Cournane
- Ministry for the Environment - Manatū Mō Te Taiao, 45 Queen Street, Auckland 1010, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, 46 Wakefield St, Auckland, 1010, New Zealand
| | - Kim M Handley
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, New Zealand
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10
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Eaton WD, McGee KM, Alderfer K, Jimenez AR, Hajibabaei M. Increase in abundance and decrease in richness of soil microbes following Hurricane Otto in three primary forest types in the Northern Zone of Costa Rica. PLoS One 2020; 15:e0231187. [PMID: 32730267 PMCID: PMC7392270 DOI: 10.1371/journal.pone.0231187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/07/2020] [Indexed: 11/26/2022] Open
Abstract
Little is known of how hurricane-induced deposition of canopy material onto tropical forest floors influences the soil microbial communities involved in decomposition of these materials. In this study, to identify how soil bacterial and fungal communities might change after a hurricane, and their possible roles in the C and N cycles, soils were collected from five 2000 m2 permanent plots in Lowland, Upland and Riparian primary forests in Costa Rica 3 months before and 7 months after Hurricane Otto damaged the forests. The soil Water, inorganic N and Biomass C increased and total organic C decreased Post-Hurricane, all of which best predicted the changes in the Post-Hurricane soil microbial communities. Post-Hurricane soils from all forest types showed significant changes in community composition of total bacteria, total fungi, and five functional groups of microbes (i.e., degrading/lignin degrading, NH4+-producing, and ammonium oxidizing bacteria, and the complex C degrading/wood rot/lignin degrading and ectomycorrhizal fungi), along with a decrease in richness in genera of all groups. As well, the mean proportion of DNA sequences (MPS) of all five functional groups increased. There were also significant changes in the MPS values of 7 different fungal and 7 different bacterial genera that were part of these functional groups. This is the first evidence that hurricane-induced deposition of canopy material is stimulating changes in the soil microbial communities after the hurricane, involving changes in specific taxonomic and functional group genera, and reduction in the community richness while selecting for dominant genera possibly better suited to process the canopy material. These changes may represent examples of taxonomic switching of functionally redundant microbial genera in response to dramatic changes in resource input. It is possible that differences in these microbial communities and genera may serve as indicators of disturbed and recovering regional soil ecosystems, and should be evaluated in the future.
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Affiliation(s)
- William D. Eaton
- Biology Department, Pace University, New York, NY, United States of America
- * E-mail:
| | - Katie M. McGee
- Department of Integrative Biology, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
| | - Kiley Alderfer
- Biology Department, Pace University, New York, NY, United States of America
| | | | - Mehrdad Hajibabaei
- Department of Integrative Biology, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
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Complete Genome Sequence of the Novel Roseimicrobium sp. Strain ORNL1, a Verrucomicrobium Isolated from the Populus deltoides Rhizosphere. Microbiol Resour Announc 2020; 9:9/27/e00617-20. [PMID: 32616646 PMCID: PMC7330248 DOI: 10.1128/mra.00617-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Roseimicrobium sp. strain ORNL1 is a soil bacterium that belongs to the phylum Verrucomicrobia and was isolated from the rhizosphere of a forest Eastern cottonwood tree, Populus deltoides, in Tennessee. Its 7.9-Mb chromosome was completely sequenced using PacBio long reads and is predicted to encode 6,288 proteins and 76 RNAs. Roseimicrobium sp. strain ORNL1 is a soil bacterium that belongs to the phylum Verrucomicrobia and was isolated from the rhizosphere of a forest Eastern cottonwood tree, Populus deltoides, in Tennessee. Its 7.9-Mb chromosome was completely sequenced using PacBio long reads and is predicted to encode 6,288 proteins and 76 RNAs.
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12
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Khan MAW, Bohannan BJM, Nüsslein K, Tiedje JM, Tringe SG, Parlade E, Barberán A, Rodrigues JLM. Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils. FEMS Microbiol Ecol 2019; 95:5211045. [PMID: 30481288 PMCID: PMC6294608 DOI: 10.1093/femsec/fiy230] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/26/2018] [Indexed: 01/28/2023] Open
Abstract
Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (-0.80 ≥ P ≥ 0.80, adjusted P < 0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H++Al3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.
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Affiliation(s)
- M A Wadud Khan
- Department of Biology, University of Texas, Arlington, TX 76019, USA
| | | | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
| | - Susannah G Tringe
- Joint Genome Institute, United States Department of Energy, Walnut Creek, CA 94598, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eloi Parlade
- Department of Land, Air and Water Resources, University of California - Davis, Davis, CA 95616, USA
| | - Albert Barberán
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721, USA
| | - Jorge L M Rodrigues
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Land, Air and Water Resources, University of California - Davis, Davis, CA 95616, USA
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14
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Kroeger ME, Delmont TO, Eren AM, Meyer KM, Guo J, Khan K, Rodrigues JLM, Bohannan BJM, Tringe SG, Borges CD, Tiedje JM, Tsai SM, Nüsslein K. New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes. Front Microbiol 2018; 9:1635. [PMID: 30083144 PMCID: PMC6064768 DOI: 10.3389/fmicb.2018.01635] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/30/2018] [Indexed: 11/17/2022] Open
Abstract
Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change.
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Affiliation(s)
- Marie E Kroeger
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Tom O Delmont
- Department of Medicine, University of Chicago, Chicago, IL, United States
| | - A M Eren
- Department of Medicine, University of Chicago, Chicago, IL, United States.,Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Kyle M Meyer
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Jiarong Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
| | - Kiran Khan
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Jorge L M Rodrigues
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, CA, United States
| | - Brendan J M Bohannan
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | | | - Clovis D Borges
- Centro de Energia Nuclear na Agricultura, University of São Paulo, Piracicaba, Brazil
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
| | - Siu M Tsai
- Centro de Energia Nuclear na Agricultura, University of São Paulo, Piracicaba, Brazil
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
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15
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Archaea in Natural and Impacted Brazilian Environments. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:1259608. [PMID: 27829818 PMCID: PMC5086508 DOI: 10.1155/2016/1259608] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/08/2016] [Indexed: 11/26/2022]
Abstract
In recent years, archaeal diversity surveys have received increasing attention. Brazil is a country known for its natural diversity and variety of biomes, which makes it an interesting sampling site for such studies. However, archaeal communities in natural and impacted Brazilian environments have only recently been investigated. In this review, based on a search on the PubMed database on the last week of April 2016, we present and discuss the results obtained in the 51 studies retrieved, focusing on archaeal communities in water, sediments, and soils of different Brazilian environments. We concluded that, in spite of its vast territory and biomes, the number of publications focusing on archaeal detection and/or characterization in Brazil is still incipient, indicating that these environments still represent a great potential to be explored.
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16
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de Menezes AB, Müller C, Clipson N, Doyle E. The soil microbiome at the Gi-FACE experiment responds to a moisture gradient but not to CO2 enrichment. MICROBIOLOGY-SGM 2016; 162:1572-1582. [PMID: 27459857 DOI: 10.1099/mic.0.000341] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The soil bacterial community at the Giessen free-air CO2 enrichment (Gi-FACE) experiment was analysed by tag sequencing of the 16S rRNA gene. No substantial effects of CO2 levels on bacterial community composition were detected. However, the soil moisture gradient at Gi-FACE had a significant effect on bacterial community composition. Different groups within the Acidobacteria and Verrucomicrobia phyla were affected differently by soil moisture content. These results suggest that modest increases in atmospheric CO2 may cause only minor changes in soil bacterial community composition and indicate that the functional responses of the soil community to CO2 enrichment previously reported at Gi-FACE are due to factors other than changes in bacterial community composition. The effects of the moisture gradient revealed new information about the relationships between poorly known Acidobacteria and Verrucomicrobia and soil moisture content. This study contrasts with the relatively small number of other temperate grassland free-air CO2 enrichment microbiome studies in the use of moderate CO2 enrichment and the resulting minor changes in the soil microbiome. Thus, it will facilitate the development of further climate change mitigation studies. In addition, the moisture gradient found at Gi-FACE contributes new knowledge in soil microbial ecology, particularly regarding the abundance and moisture relationships of the soil Verrucomicrobia.
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Affiliation(s)
- Alexandre B de Menezes
- Peel Building, School of Environment & Life Sciences, University of Salford, Salford M5 4WT, UK
| | - Christoph Müller
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.,Department of Plant Ecology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Nicholas Clipson
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Evelyn Doyle
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
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Pajares S, Bohannan BJM. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils. Front Microbiol 2016; 7:1045. [PMID: 27468277 PMCID: PMC4932190 DOI: 10.3389/fmicb.2016.01045] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/22/2016] [Indexed: 01/08/2023] Open
Abstract
Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.
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Affiliation(s)
- Silvia Pajares
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de MéxicoCoyoacán, Mexico
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18
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Navarrete AA, Venturini AM, Meyer KM, Klein AM, Tiedje JM, Bohannan BJM, Nüsslein K, Tsai SM, Rodrigues JLM. Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon. Front Microbiol 2015; 6:1443. [PMID: 26733981 PMCID: PMC4686610 DOI: 10.3389/fmicb.2015.01443] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/03/2015] [Indexed: 11/13/2022] Open
Abstract
Members of the phylum Acidobacteria are among the most abundant soil bacteria on Earth, but little is known about their response to environmental changes. We asked how the relative abundance and biogeographic patterning of this phylum and its subgroups responded to forest-to-pasture conversion in soils of the western Brazilian Amazon. Pyrosequencing of 16S rRNA genes was employed to assess the abundance and composition of the Acidobacteria community across 54 soil samples taken using a spatially nested sampling scheme at the landscape level. Numerically, Acidobacteria represented 20% of the total bacterial community in forest soils and 11% in pasture soils. Overall, 15 different Acidobacteria subgroups of the current 26 subgroups were detected, with Acidobacteria subgroups 1, 3, 5, and 6 accounting together for 87% of the total Acidobacteria community in forest soils and 75% in pasture soils. Concomitant with changes in soil chemistry after forest-to-pasture conversion—particularly an increase in properties linked to soil acidity and nutrient availability—we observed an increase in the relative abundances of Acidobacteria subgroups 4, 10, 17, and 18, and a decrease in the relative abundances of other Acidobacteria subgroups in pasture relative to forest soils. The composition of the total Acidobacteria community as well as the most abundant Acidobacteria subgroups (1, 3, 5, and 6) was significantly more similar in composition across space in pasture soils than in forest soils. These results suggest that preponderant responses of Acidobacteria subgroups, especially subgroups 1, 3, 4, 5, and 6, to forest-to-pasture conversion effects in soils could be used to define management-indicators of agricultural practices in the Amazon Basin. These acidobacterial responses are at least in part through alterations on acidity- and nutrient-related properties of the Amazon soils.
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Affiliation(s)
- Acacio A Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo Piracicaba, Brazil
| | - Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo Piracicaba, Brazil
| | - Kyle M Meyer
- Department of Biology, Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | - Ann M Klein
- Department of Biology, Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Center for Microbial Ecology, Michigan State University East Lansing, MI, USA
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo Piracicaba, Brazil
| | - Jorge L M Rodrigues
- Department of Land, Air and Water Resources, University of California, Davis Davis, CA, USA
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