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Zhang S, Hu W, Zhang J, Yu G, Liu Y, Kong Z, Wu L. Long-term cultivation reduces soil carbon storage by altering microbial network complexity and metabolism activity in macroaggregates. Sci Total Environ 2024; 930:172788. [PMID: 38677431 DOI: 10.1016/j.scitotenv.2024.172788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/14/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Cultivation alters soil aggregation, microbial compositions and the potential for carbon sequestration in cropland soils. However, the specific effects of long-term cultivation and the underlying mechanisms on soil organic carbon (SOC) storage at different aggregate sizes remain poorly understood. We characterized the dynamics of SOC storage in macroaggregates (>0.25 mm) and microaggregates (<0.25 mm) across four paddy soils successively cultivated for 60, 100, 125, and 150 years. Microbial community compositions, network patterns, enzyme activities and carbon use efficiency (CUE) were examined to elucidate the underlying microbial pathways governing SOC storage. The results showed that prolonged cultivation led to an average reduction of 45 % in SOC storage, particularly in macroaggregates. Partial least squares path modeling revealed that shifts in microorganisms in macroaggregates explained almost 80 % of the variation in SOC storage. Specifically, variations in fungal composition and decreased complexity of microbial interaction networks were strongly correlated with SOC storage. Fungal community and microbial interactions also indirectly affected SOC storage by positively correlating with extracellular enzyme activity. Moreover, bacterial composition indirectly regulated SOC storage by positively correlating with carbon use efficiency. Our findings indicated that the macroaggregate-associated microbial interactions and the metabolism activities had significant implications for SOC sequestration in paddy fields. We suggest that implementation of management practices targeted at improvement of these microbial attributes could enhance agroecosystems sustainability.
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Affiliation(s)
- Shan Zhang
- School of Life Sciences, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Wanjin Hu
- School of Life Sciences, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Jinting Zhang
- School of Life Sciences, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Guanjun Yu
- Jiangxi Poyang Lake Nanji Wetland National Nature Reserve Authority, Nanchang 330038, China
| | - Yizhen Liu
- School of Life Sciences, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China.
| | - Zhaoyu Kong
- School of Life Sciences, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Lan Wu
- School of Life Sciences, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China.
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Wang T, Hu C, Zhou T, Zhang Y, Hu H, Zou L, Zhou W, Gao H, Ren X, Wang J, Hu S. Artificial utilization of saline-sodic land promotes carbon stock: The importance of large macroaggregates. J Environ Manage 2024; 354:120343. [PMID: 38364541 DOI: 10.1016/j.jenvman.2024.120343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/08/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024]
Abstract
Soil aggregates are essential functional units involved in soil carbon sequestration, particularly in saline-sodic soils prone to severe carbon loss. In the present study, the distribution of aggregate-associated carbon fractions and their influencing factors were investigated after artificial utilization of saline soil in the Songnen Plain, Northeast China. Physicochemical properties, enzymatic activities, and bacterial communities were measured in various hierarchical aggregates among two natural land-use types (saline wasteland and degraded grassland) and three anthropogenic land-use types (artificial forest, upland field, and paddy field). The results indicated that, compared to saline wasteland, anthropogenic land use was witnessed an increase in macroaggregate proportions, and PF in large macroaggregates increased the most, while UF and FL were mainly increased in small macroaggregates. After transforming from natural land to anthropogenic land, the aggregate-associated carbon fractions (total organic carbon, readily soluble organic carbon, dissolved organic carbon, and microbial biomass carbon) increased, especially in small macroaggregates. All enzyme activities increased after artificial utilization, hydrolase (urease, amylase, and invertase), catalase, and β-glucosidase activities were highest in the small macroaggregates. Bacterial biomass was increased in all three aggregate types compared to natural land. Due to the influence of various factors on soil carbon storage, through partial least squares path modeling revealed that large macroaggregates were conducive to carbon storage. These findings suggested that artificial utilization of saline soil can increase large macroaggregate proportions and the abundance of aggregate-associated carbon, resulting in increased soil carbon stocks, with PF having the greatest carbon sequestration capacity.
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Affiliation(s)
- Tianhao Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-Control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Canmin Hu
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-Control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Tairan Zhou
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-Control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Yun Zhang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-Control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Hao Hu
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-Control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Li Zou
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-Control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Wenfeng Zhou
- Department of Applied Chemistry, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Haixiang Gao
- Department of Applied Chemistry, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Xueqin Ren
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-Control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-Control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
| | - Shuwen Hu
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-Control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
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3
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Mousavi SA, Ramula S. The invasive legume Lupinus polyphyllus has minor site-specific impacts on the composition of soil bacterial communities. Ecol Evol 2024; 14:e11030. [PMID: 38357596 PMCID: PMC10864723 DOI: 10.1002/ece3.11030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 01/26/2024] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
Plant invasions can have major impacts on ecosystems, both above- and belowground. In particular, invasions by legumes, which often host nitrogen-fixing symbionts (rhizobia), are known to modify soil bacterial communities. Here, we examined the effect of the invasive herbaceous legume Lupinus polyphyllus on the alpha diversity and community composition of soil bacteria. We also explored the relationships between these bacterial communities and vegetation cover, the cover of other (non-invasive) legumes, or the number of vascular plants present. For this, we sampled rhizosphere soil and surveyed vegetation from ten paired sites (uninvaded versus invaded more than 10 years ago) in southwestern Finland, and identified bacterial DNA using 16S rRNA gene amplicon sequencing. The presence of the plant invader and the three vegetation variables considered had no effect on the alpha diversity of soil bacteria in terms of bacterial richness or Shannon and Inverse Simpson diversity indices. However, the composition of soil bacterial communities differed between invaded and uninvaded soils at four out of the ten sites. Interestingly, the relative abundances of the top bacterial families in invaded and uninvaded soils were inconsistent across sites, including for legume-associated rhizobia in the family Bradyrhizobiaceae. Other factors-such as vegetation cover, legume cover (excluding L. polyphyllus), number of plant species-also explained a small proportion of the variation in bacterial community composition. Our findings indicate that L. polyphyllus has the potential to modify the composition of local soil bacterial community, at least in sites where it has been present for more than a decade.
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Affiliation(s)
| | - Satu Ramula
- Department of BiologyUniversity of TurkuTurkuFinland
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Liu XJA, Han S, Frey SD, Melillo JM, Zhou J, DeAngelis KM. Microbial responses to long-term warming differ across soil microenvironments. ISME Commun 2024; 4:ycae051. [PMID: 38699060 PMCID: PMC11065356 DOI: 10.1093/ismeco/ycae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024]
Abstract
Soil carbon loss is likely to increase due to climate warming, but microbiomes and microenvironments may dampen this effect. In a 30-year warming experiment, physical protection within soil aggregates affected the thermal responses of soil microbiomes and carbon dynamics. In this study, we combined metagenomic analysis with physical characterization of soil aggregates to explore mechanisms by which microbial communities respond to climate warming across different soil microenvironments. Long-term warming decreased the relative abundances of genes involved in degrading labile compounds (e.g. cellulose), but increased those genes involved in degrading recalcitrant compounds (e.g. lignin) across aggregate sizes. These changes were observed in most phyla of bacteria, especially for Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes. Microbial community composition was considerably altered by warming, leading to declined diversity for bacteria and fungi but not for archaea. Microbial functional genes, diversity, and community composition differed between macroaggregates and microaggregates, indicating the essential role of physical protection in controlling microbial community dynamics. Our findings suggest that microbes have the capacity to employ various strategies to acclimate or adapt to climate change (e.g. warming, heat stress) by shifting functional gene abundances and community structures in varying microenvironments, as regulated by soil physical protection.
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Affiliation(s)
- Xiao Jun A Liu
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, United States
- Institute for Environmental Genomics and School of Biological Sciences, University of Oklahoma , Norman, OK 73019, United States
| | - Shun Han
- Institute for Environmental Genomics and School of Biological Sciences, University of Oklahoma , Norman, OK 73019, United States
| | - Serita D Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, United States
| | - Jerry M Melillo
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA 02543, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics and School of Biological Sciences, University of Oklahoma , Norman, OK 73019, United States
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- School of Civil Engineering and Environmental Sciences and School of Computer Science, University of Oklahoma, Norman, OK 73019, United States
| | - Kristen M DeAngelis
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, United States
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Ju W, Fang L, Shen G, Delgado-Baquerizo M, Chen J, Zhou G, Ma D, Bing H, Liu L, Liu J, Jin X, Guo L, Tan W, Blagodatskaya E. New perspectives on microbiome and nutrient sequestration in soil aggregates during long-term grazing exclusion. Glob Chang Biol 2024; 30:e17027. [PMID: 37946660 DOI: 10.1111/gcb.17027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Grazing exclusion alters grassland soil aggregation, microbiome composition, and biogeochemical processes. However, the long-term effects of grazing exclusion on the microbial communities and nutrient dynamics within soil aggregates remain unclear. We conducted a 36-year exclusion experiment to investigate how grazing exclusion affects the soil microbial community and the associated soil functions within soil aggregates in a semiarid grassland. Long-term (36 years) grazing exclusion induced a shift in microbial communities, especially in the <2 mm aggregates, from high to low diversity compared to the grazing control. The reduced microbial diversity was accompanied by instability of fungal communities, extended distribution of fungal pathogens to >2 mm aggregates, and reduced carbon (C) sequestration potential thus revealing a negative impact of long-term GE. In contrast, 11-26 years of grazing exclusion greatly increased C sequestration and promoted nutrient cycling in soil aggregates and associated microbial functional genes. Moreover, the environmental characteristics of microhabitats (e.g., soil pH) altered the soil microbiome and strongly contributed to C sequestration. Our findings reveal new evidence from soil microbiology for optimizing grazing exclusion duration to maintain multiple belowground ecosystem functions, providing promising suggestions for climate-smart and resource-efficient grasslands.
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Affiliation(s)
- Wenliang Ju
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences, Ministry of Water Resources, Yangling, China
- School of Environment, Tsinghua University, Beijing, China
| | - Linchuan Fang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences, Ministry of Water Resources, Yangling, China
- Key Laboratory of Green Utilization of Critical Non-metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan, China
| | - Guoting Shen
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Guiyao Zhou
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Dengke Ma
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences, Ministry of Water Resources, Yangling, China
| | - Haijian Bing
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
| | - Lei Liu
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ji Liu
- Hubei Province Key Laboratory for Geographical Process Analysis and Simulation, Central China Normal University, Wuhan, China
| | - Xiaolian Jin
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences, Ministry of Water Resources, Yangling, China
| | - Liang Guo
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences, Ministry of Water Resources, Yangling, China
| | - Wenfeng Tan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Evgenia Blagodatskaya
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
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Chen Y, Xu Y, Ma Y, Lin J, Ruan A. Microbial community structure and its driving mechanisms in the Hangbu estuary of Chaohu Lake under different sedimentary areas. Environ Res 2023; 238:117153. [PMID: 37726029 DOI: 10.1016/j.envres.2023.117153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/02/2023] [Accepted: 09/13/2023] [Indexed: 09/21/2023]
Abstract
Estuaries are known for their high ecological diversity and biological productivity. Sediment microorganisms, as crucial components of estuarine ecosystems, play a pivotal role in reflecting the intricate and dynamic ecological niches. However, our research on microbial community characteristics in estuarine ecosystems under different sedimentary types remains limited. In this study, we collected a total of 27 samples from three sampling sites at Hangbu estuary in Chaohu Lake, and three sedimentary areas were classified based on the overlying water flow conditions and sediment particle properties to elucidate their microbial community structure, environmental drivers, assembly processes, and co-occurrence network characteristics. Our results showed significant differences in microbial community composition and diversity among three sedimentary areas. Redundancy analysis indicated that the differences in microbial community composition at the OTU level among the three sedimentary areas were mainly determined by nitrate-nitrogen, temperature, and water content. Phylogenetic bin-based null model analysis revealed that temperature was a key factor influencing deterministic processes among the three sedimentary areas, while stochastic processes predominantly governed the assembly of microbial communities. In addition, co-occurrence network analysis demonstrated that the network in the hydraulically driven sedimentary area of the lake, consisting mainly of medium and fine silt, had the highest complexity, stability, and cohesion, but was missing potential keystone taxa. The remaining two sedimentary areas had 5 and 8 potential keystone taxa, respectively. Overall, our study proposes the delineation of sedimentary types and comprehensively elucidates the microbial community characteristics under different sedimentary areas, providing a new perspective for studying sediment microbial community structure and helping future scholars systematically study ecological dynamics in estuaries.
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Affiliation(s)
- Yang Chen
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Yaofei Xu
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Yunmei Ma
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Jie Lin
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Aidong Ruan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China.
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Min K, Zheng T, Zhu X, Bao X, Lynch L, Liang C. Bacterial community structure and assembly dynamics hinge on plant litter quality. FEMS Microbiol Ecol 2023; 99:fiad118. [PMID: 37771081 DOI: 10.1093/femsec/fiad118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 06/29/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023] Open
Abstract
Litter decomposition is a fundamental ecosystem process controlling the biogeochemical cycling of energy and nutrients. Using a 360-day lab incubation experiment to control for environmental factors, we tested how litter quality (low C/N deciduous vs. high C/N coniferous litter) governed the assembly and taxonomic composition of bacterial communities and rates of litter decomposition. Overall, litter mass loss was significantly faster in soils amended with deciduous (DL) rather than coniferous (CL) litter. Communities degrading DL were also more taxonomically diverse and exhibited stochastic assembly throughout the experiment. By contrast, alpha-diversity rapidly declined in communities exposed to CL. Strong environmental selection and competitive biological interactions induced by molecularly complex, nutrient poor CL were reflected in a transition from stochastic to deterministic assembly after 180 days. Constraining how the diversity and assembly of microbial populations modulates core ecosystem processes, such as litter decomposition, will become increasingly important under novel climate conditions, and as policymakers and land managers emphasize soil carbon sequestration as a key natural climate solution.
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Affiliation(s)
- Kaikai Min
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Tiantian Zheng
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
| | - Xuefeng Zhu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
| | - Xuelian Bao
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
| | - Laurel Lynch
- Department of Soil and Water Systems, University of Idaho, Moscow, ID 83844, USA
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
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Lagos S, Tsetsekos G, Mastrogianopoulos S, Tyligada M, Diamanti L, Vasileiadis S, Sotiraki S, Karpouzas DG. Interactions of anthelmintic veterinary drugs with the soil microbiota: Toxicity or enhanced biodegradation? Environ Pollut 2023; 334:122135. [PMID: 37406753 DOI: 10.1016/j.envpol.2023.122135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Anthelmintic (AH) compounds are used to control gastrointestinal nematodes (GINs) in livestock production. They are only partially metabolized in animals ending in animal excreta whose use as manures leads to AH dispersal in agricultural soils. Once in soil, AHs interact with soil microorganisms, with the outcome being either detrimental, or beneficial. We aimed to disentangle the mechanisms of these complex interactions. Two soils previously identified as « fast » or « slow», regarding the degradation of albendazole (ABZ), ivermectin (IVM), and eprinomectin (EPM), were subjected to repeated applications at two dose rates (1, 2 mg kg-1and 10, 20 mg kg-1). We hypothesized that this application scheme will lead to enhanced biodegradation in «fast » soils and accumulation and toxicity in «slow » soils. Repeated application of ABZ resulted in different transformation pathways in the two soils and a clear acceleration of its degradation in the «fast » soil only. In contrast residues of IVM and EPM accumulated in both soils. ABZ was the sole AH that induced a consistent reduction in the abundance of total fungi and crenarchaea. In addition, inhibition of nitrification and reduction in the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) by all AHs was observed, while commamox bacteria were less responsive. Amplicon sequencing analysis showed dose-depended shifts in the diversity of bacteria, fungi, and protists in response to AHs application. ABZ presented the most consistent effect on the abundance and diversity of most microbial groups. Our findings provide first evidence for the unexpected toxicity of AHs on key soil microbial groups that might have to be considered in a regulatory context.
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Affiliation(s)
- Stathis Lagos
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - Georgios Tsetsekos
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - Spyridon Mastrogianopoulos
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - Maria Tyligada
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - Lamprini Diamanti
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - Sotirios Vasileiadis
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - Smaragda Sotiraki
- Laboratory of Parasitology, Hellenic Agricultural Organization-Demeter, Veterinary Research Institute, 57001, Thermi, Greece
| | - Dimitrios G Karpouzas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece.
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9
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Ossanna LQR, Serrano K, Jennings LL, Dillon J, Maier RM, Neilson JW. Progressive belowground soil development associated with sustainable plant establishment during copper mine waste revegetation. Appl Soil Ecol 2023; 186:104813. [PMID: 36844191 PMCID: PMC9956965 DOI: 10.1016/j.apsoil.2023.104813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Critical to the environmental sustainability of hard rock mining is the reclamation of disturbed lands following mine closure through revegetation. Improved understanding of associations between above- and belowground processes that characterize successful plant establishment is critical to the implementation of more efficient revegetation strategies for nutrient-poor mine waste materials. The specific objective of this five-year temporal study was to identify progressive biotic and abiotic indicators of primary soil development on mine waste rock (WR) on a slope hydroseeded with native plant species and to quantify comparative effects of plant lifeform on soil development. Aboveground plant diversity and belowground substrate properties were measured annually at 67 m intervals along transects following the slope contour. Seeded WR was compared to unseeded WR and the adjacent native ecosystem. A temporal increase in WR microbial biomass was observed in seeded WR relative to unseeded areas. Microbial community analysis found the unseeded WR to be defined by oligotrophic microbes, whereas targeted grass and shrub root zones samples demonstrated significant increases in specific cellulose and lignin degrading and N-cycling phylotypes. More extensive chemical and biological fertility development was observed in shrub root zones relative to grass. Ten chemical and biological indicators increased significantly in shrub WR relative to unseeded WR, whereas grass WR was only enriched in bacterial 16S rRNA gene copy number/g substrate and bacterial/archaeal and fungal diversity. In addition, the shrub root zone had significantly higher nitrogen-cycling potential than grass root zones or unseeded WR. Thus, both grasses and shrubs improve belowground WR development; however, shrub establishment had greater fertility outcomes. Concurrent belowground fertility development is critical to sustainable plant establishment. Coupled evaluation of above- and belowground metrics provides an improved quantitative assessment of revegetation progress and a valuable tool to guide management decisions.
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Affiliation(s)
- Lia Q. R. Ossanna
- Environmental Science Department, University of Arizona, Tucson, AZ, 85721, USA
| | - Karen Serrano
- Environmental Science Department, University of Arizona, Tucson, AZ, 85721, USA
| | - Lydia L. Jennings
- Environmental Science Department, University of Arizona, Tucson, AZ, 85721, USA
| | - Jesse Dillon
- Cedar Creek Associates, Inc., Fort Collins, CO, 80527, USA
| | - Raina M. Maier
- Environmental Science Department, University of Arizona, Tucson, AZ, 85721, USA
| | - Julia W. Neilson
- Environmental Science Department, University of Arizona, Tucson, AZ, 85721, USA
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Yang N, Hou X, Li Y, Zhang H, Wang J, Hu X, Zhang W. Inter-basin water diversion homogenizes microbial communities mainly through stochastic assembly processes. Environ Res 2023; 223:115473. [PMID: 36787823 DOI: 10.1016/j.envres.2023.115473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/14/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Inter-basin water transfer is an effective manner to achieve the optimal allocation of water resources, while accompanied by some ecological effects. The responses of microorganisms to water diversion and the ecological processes in regulating the community assembly are still unclear. Taking the eastern route of South-to-North Water Diversion Project as the study area, we investigated the microbial community patterns and the underlying assemblage processes in habitats with different hydrological connectivity, including isolated lakes, connected lakes and man-made canal. The results showed that microbial communities in the canal had higher diversity, lower dissimilarity, weaker compositional variation, and stronger co-occurrence patterns compared with that in the connected and isolated lakes. These findings suggested that the increase of connectivity among natural aquatic habitats due to water diversion can homogenize microbial communities and reduce microbial heterogeneity. The neutral and null models demonstrated the importance of stochastic processes in shaping microbial community assembly. Dispersal limitation and variable selection were the predominant mechanisms structuring microbial communities in the isolated lakes. Due to the homogenized environmental condition and the enhanced hydrologic connectivity in the canal and the connected lakes, microbial communities had higher dispersal capability and ecological drift occurred more frequently in these lotic habitats. The variations in microbial community structure were mainly driven by biotic ecological succession than abiotic factors, with positive and negative cohesion explained 63% and 25% of variability, respectively. Six taxa were considered as the potential introduced microorganisms, which may favor the nutrient biogeochemical cycling and the organic matter degradation, but may also bring ecological risks. Overall, this study provides a deeper understanding of the ecological consequences of inter-basin water diversion, and helps the regulation and management of these projects.
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Affiliation(s)
- Nan Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Xing Hou
- Institute of Water Science and Technolagy, Hohai University, Nanjing, 211106, China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Institute of Water Science and Technolagy, Hohai University, Nanjing, 211106, China.
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Jun Wang
- Jiangsu Institute of Water Resources and Hydropower Research, Nanjing, 210017, China
| | - Xiaodong Hu
- Jiangsu Institute of Water Resources and Hydropower Research, Nanjing, 210017, China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
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11
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Stefani F, Beguin J, Paré D, Morency MJ, Martineau C, Fortin JA, Thiffault N, Séguin A. Does wood mulch trigger microbially mediated positive plant-soil feedback in degraded boreal forest sites? A post hoc study. Front Plant Sci 2023; 14:1122445. [PMID: 37206972 PMCID: PMC10191178 DOI: 10.3389/fpls.2023.1122445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/15/2023] [Indexed: 05/21/2023]
Abstract
Introduction Reforestation of degraded lands in the boreal forest is challenging and depends on the direction and strength of the plant-soil feedback (PSF). Methods Using a gradient in tree productivity (null, low and high) from a long-term, spatially replicated reforestation experiment of borrow pits in the boreal forest, we investigated the interplay between microbial communities and soil and tree nutrient stocks and concentrations in relation to a positive PSF induced by wood mulch amendment. Results Three levels of mulch amendment underlie the observed gradient in tree productivity, and plots that had been amended with a continuous layer of mulch 17 years earlier showed a positive PSF with trees up to 6 m tall, a closed canopy, and a developing humus layer. The average taxonomic and functional composition of the bacterial and fungal communities differed markedly betweenlow- and high-productivity plots. Trees in high-productivity plots recruited a specialized soil microbiome that was more efficient at nutrient mobilization and acquisition. These plots showed increases in carbon (C), calcium (Ca), nitrogen (N), potassium (K), and phosphorus (P) stocks and as well as bacterial and fungal biomass. The soil microbiome was dominated by taxa from the fungal genus Cortinarius and the bacterial family Chitinophagaceae, and a complex microbial network with higher connectivity and more keystone species supported tree productivity in reforested plots compared to unproductive plots. Discussion Therefore, mulching of plots resulted in a microbially mediated PSF that enhances mineral weathering and non-symbiotic N fixation, and in turn helps transform unproductive plots into productive plots to ensure rapid restoration of the forest ecosystem in a harsh boreal environment.
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Affiliation(s)
- Franck Stefani
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- *Correspondence: Franck Stefani, ; David Paré,
| | - Julien Beguin
- Institut de recherche sur les forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
| | - David Paré
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
- *Correspondence: Franck Stefani, ; David Paré,
| | - Marie-Josée Morency
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Christine Martineau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - J. André Fortin
- Université Laval, Faculté de foresterie, de géographie et de géomatique, Département des sciences du bois et de la forêt, Québec, QC, Canada
| | - Nelson Thiffault
- Natural Resources Canada, Canadian Forest Service, Canadian Wood Fibre Centre, Québec, QC, Canada
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
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12
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Keuschnig C, Martins JMF, Navel A, Simonet P, Larose C. Micro-fractionation shows microbial community changes in soil particles below 20 μm. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1091773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
IntroductionMicro-scale analysis of microbes in soil is essential to the overall understanding of microbial organization, interactions, and ecosystem functioning. Soil fractionation according to its aggregated structure has been used to access microbial habitats. While bacterial communities have been extensively described, little is known about the fungal communities at scales relevant to microbial interactions.MethodsWe applied a gentle soil fractionation method to preserve stable aggregated structures within the range of micro-aggregates and studied fungal and bacterial communities as well as nitrogen cycling potentials in the pristine Rothamsted Park Grass soil (bulk soil) as well as in its particle size fractions (PSFs; >250 μm, 250–63 μm, 63–20 μm, 20–2 μm, <2 μm, and supernatant).ResultsOverall bacterial and fungal community structures changed in PSFs below 20 μm. The relative abundance of Basidiomycota decreased with decreasing particle size over the entire measure range, while Ascomycota showed an increase and Mucoromycota became more prominent in particles below 20 μm. Bacterial diversity was found highest in the < 2 μm fraction, but only a few taxa were washed-off during the procedure and found in supernatant samples. These taxa have been associated with exopolysaccharide production and biofilm formation (e.g., Pseudomonas, Massilia, Mucilaginibacter, Edaphobaculum, Duganella, Janthinobacterium, and Variovorax). The potential for nitrogen reduction was found elevated in bigger aggregates.DiscussionThe observed changes below 20 μm particle are in line with scales where microbes operate and interact, highlighting the potential to focus on little researched sub-fractions of micro-aggregates. The applied method shows potential for use in studies focusing on the role of microbial biofilms in soil and might also be adapted to research various other soil microbial functions. Technical advances in combination with micro-sampling methods in soil promise valuable output in soil studies when particles below 20 μm are included.
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13
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Zhang L, Cheng Y, Qian Y, Ding T, Li J. Bisphenol S degradation in soil and the dynamics of microbial community associated with degradation. Sci Total Environ 2022; 846:157451. [PMID: 35868379 DOI: 10.1016/j.scitotenv.2022.157451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Bisphenol S (BPS) has been widely applied as a replacement for BPA in industrial application, leading to the frequent detection in the environment. However, its impact on soil microbial communities has not been well reported. Here, effects of BPS exposure on soil microbial communities in the presence of polystyrene (PS) microplastics were revealed. Rapid degradation of BPS occurred with a degradation rate of up to 98.9 ± 0.001 % at 32 d. The presence of BPS reduced the diversity of soil microbial communities, and changed community structures. After BPS treatment, Proteobacteria, and its members Methylobacillus, Rhodobacteraceae and Mesorhizobium became dominant, and were considered as potential biomarkers indicating BPS contamination. Co-occurrence network analysis revealed the increased relationships of certain groups of microbes after BPS treatment. The resultant low stability and resilience towards environment disturbance of microbial community networks implied the biotoxicity of BPS towards soil ecosystems. The degradation and biotoxicity of BPS (p > 0.05) in soil was not affected by the presence of PS. Our findings showed that exposure to BPS could reshape soil microbial communities and impair the robustness of microbial co-occurrence networks.
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Affiliation(s)
- Lili Zhang
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yanan Cheng
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yiguang Qian
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Tengda Ding
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Juying Li
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China.
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14
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Li X, Zhang Z, Lü X, Li Y, Jin K, van der Putten WH. Soil aggregate microbiomes steer plant community overyielding in ungrazed and intensively grazed grassland soils. J Environ Manage 2022; 321:115919. [PMID: 36001914 DOI: 10.1016/j.jenvman.2022.115919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
Plant and soil microbial community composition play a central role in maintaining ecosystem functioning. Most studies have focused on soil microbes in the bulk soil, the rhizosphere and inside plant roots, however, less is known about the soil community that exists within soil aggregates, and how these soil communities influence plant biomass production. Here, using field-conditioned soil collected from experimental ungrazed and grazed grasslands in Inner Mongolia, China, we examined the composition of microbiomes inside soil aggregates of various size classes, and determined their roles in plant-soil feedbacks (PSFs), diversity-productivity relationships, and diversity-dependent overyielding. We found that grazing induced significantly positive PSF effects, which appeared to be mediated by mycorrhizal fungi, particularly under plant monocultures. Despite this, non-additive effects of microbiomes within different soil aggregates enhanced the strength of PSF under ungrazed grassland, but decreased PSF strength under intensively grazed grassland. Plant mixture-related increases in PSF effects markedly enhanced diversity-dependent overyielding, primarily due to complementary effects. Selection effects played far less of a role. Our work suggests that PSF contributes to diversity-dependent overyielding in grasslands via non-additive effects of microbiomes within different soil aggregates. The implication of our work is that assessing the effectiveness of sustainable grassland restoration and management on soil properties requires inspection of soil aggregate size-specific microbiomes, as these are relevant determinants of the feedback interactions between soil and plant performance.
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Affiliation(s)
- Xiliang Li
- Key Laboratory of Grassland Ecology and Restoration, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010, China; Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6700AB, the Netherlands
| | - Zhen Zhang
- Key Laboratory of Grassland Ecology and Restoration, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010, China
| | - Xiaotao Lü
- Erguna Forest-Steppe Ecotone Research Station, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Yuanheng Li
- Key Laboratory of Grassland Ecology and Restoration, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010, China.
| | - Ke Jin
- Key Laboratory of Grassland Ecology and Restoration, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010, China
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6700AB, the Netherlands; Department of Nematology, Wageningen University & Research, Wageningen 6700 ES, the Netherlands
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15
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Satish L, Barak H, Keren G, Yehezkel G, Kushmaro A, Ben-dov E, Kagan-zur V, Barak Z, Sitrit Y. The Microbiome Structure of the Symbiosis between the Desert Truffle Terfezia boudieri and Its Host Plant Helianthemum sessiliflorum. J Fungi (Basel) 2022; 8:1062. [PMID: 36294627 PMCID: PMC9605525 DOI: 10.3390/jof8101062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/17/2022] Open
Abstract
The desert truffle Terfezia boudieri is an ascomycete fungus that forms ect-endomycorrhiza in the roots of plants belonging to Cistaceae. The fungus forms hypogeous edible fruit bodies, appreciated as gourmet food. Truffles and host plants are colonized by various microbes, which may contribute to their development. However, the diversity and composition of the bacterial community under field conditions in the Negev desert are still unknown. The overall goal of this research was to identify the rhizosphere microbial community supporting the establishment of a symbiotic association between T. boudieri and Helianthemum sessiliflorum. The bacterial community was characterized by fruiting bodies, mycorrhized roots, and rhizosphere soil. Based on next-generation sequencing meta-analyses of the 16S rRNA gene, we discovered diverse bacterial communities of fruit bodies that differed from those found in the roots and rhizosphere. Families of Proteobacteria, Planctomycetes, and Actinobacteria were present in all four samples. Alpha diversity analysis revealed that the rhizosphere and roots contain significantly higher bacterial species numbers compared to the fruit. Additionally, ANOSIM and PCoA provided a comparative analysis of the bacterial taxa associated with fruiting bodies, roots, and rhizosphere. The core microbiome described consists of groups whose biological role triggers important traits supporting plant growth and fruit body development.
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16
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Zhang Y, Hui K, Li Y, Yuan Y, Tan W. Electron transfer capacity of humic acid in soil micro and macro aggregates in response to mulching years. Sci Total Environ 2022; 831:154927. [PMID: 35367553 DOI: 10.1016/j.scitotenv.2022.154927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/26/2022] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Abstract
Plastic film mulching can help farmers meet food production requirements and even increase output. Although the environmental impact of this mulch has received attention, uncertainty remains about certain soil components and the course of its long-term effects. In particular, it is not clear whether the long-term use of mulching film will affect the electron transfer capacity (ETC) of natural organic matter in the soil. This study evaluated the electron-accepting capacity (EAC) and electron-donating capacity (EDC) of soil humic acid (HA) in different-size aggregates in response to different film mulching years (0-6 years). The EAC of HA in the soil showed a downward trend as mulching years increased, while the EDC fluctuated. EAC decline in microaggregates (MIA) was more significant than that of macroaggregates (MAA). Film mulching changes the physical and chemical properties of soil and the activity of enzymes, changes the chemical structure of HA, and ultimately affects HA electron transfer. In addition, compared with that in MAA, the chemical structure of soil HA in MIA has a stronger correlation with enzyme activity and ETC and thus is more significantly affected by mulching. These results provide an in-depth understanding of the role of HA in soil aggregates of different sizes in processes related to the agricultural soil environment under mulching conditions.
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Affiliation(s)
- Yifan Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China; State Key Laboratory of Environmental Criteria and Risk Assessment, State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Kunlong Hui
- State Key Laboratory of Environmental Criteria and Risk Assessment, State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Yanhong Li
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Ying Yuan
- State Key Laboratory of Environmental Criteria and Risk Assessment, State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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17
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Smercina D, Zambare N, Hofmockel K, Sadler N, Bredeweg EL, Nicora C, Markillie LM, Aufrecht J. Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics. Microorganisms 2022; 10:microorganisms10050944. [PMID: 35630387 PMCID: PMC9146112 DOI: 10.3390/microorganisms10050944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 02/01/2023] Open
Abstract
The dynamics of microbial processes are difficult to study in natural soil, owing to the small spatial scales on which microorganisms operate and to the opacity and chemical complexity of the soil habitat. To circumvent these challenges, we have created a 3D-bioprinted habitat that mimics aspects of natural soil aggregates while providing a chemically defined and translucent alternative culturing method for soil microorganisms. Our Synthetic Soil Aggregates (SSAs) retain the porosity, permeability, and patchy resource distribution of natural soil aggregates—parameters that are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution genomics, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a model co-culture microbial community and find that it is significantly different from the spatial organization of the same community in liquid culture, indicating a potential for SSAs to reproduce naturally occurring emergent community phenotypes. The SSAs have the potential as a tool to help researchers quantify microbial scale processes in situ and achieve high-resolution data from the interplay between environmental properties and microbial ecology.
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18
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Xiong X, Liao H, Xing Y, Han X, Wang W, Wan W, Huang Q, Chen W. Soil Aggregates and Fertilizer Treatments Drive Bacterial Interactions via Interspecies Niche Overlap. Microbiol Spectr 2022; 10:e0252421. [PMID: 35234512 PMCID: PMC8941866 DOI: 10.1128/spectrum.02524-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 02/02/2022] [Indexed: 12/23/2022] Open
Abstract
Bacterial interactions play significant roles in ecological functions in responding to anthropogenic interference and soil structure changes. However, it remains largely unknown how fertilizer regimes and soil particle sizes drive bacterial interactions. To evaluate bacterial interaction patterns in soil aggregates under long-term fertilizer treatments, we sampled nine bacterial co-occurrence communities and compared the difference between interspecies resource consumption patterns and network structure. Despite the differences between fertilizer treatments, the negative correlation ratios of interaction networks in soil aggregates were macroaggregates > microaggregates > silt + clays. Likewise, NPK-supplement (chemical fertilizer) had also decreased the number of positive correlations of the interaction network than M-supplement (organic fertilizer), regardless of the size of soil aggregates. Linear model analysis revealed that interspecies trophic patterns, including niche overlap and nestedness, drove bacterial competition in the interaction networks. Most importantly, interspecies niche overlap may be the intrinsic factor in the effects of fertilizer treatments and soil aggregates on bacterial interactions. This study enhances our understanding of the potential for changes in species trophic patterns and might guide the promotion of land management. IMPORTANCE Despite that the influence of soil structure and fertilizer treatments on the bacterial community has been widely studied, how they drive interspecies interactions has not been largely explored. Connectance and nestedness were significantly correlated with bacterial interactions, but no differences were found in different soil aggregates and fertilizer treatments. However, interspecies niche overlap could respond to soil aggregates and fertilizer treatments and ultimately drive the bacterial interactions. This study enhances our understanding of the mechanism of microbial interactions and highlights the importance of trophic patterns in the bacterial community. Our findings extend knowledge for nutrient availability on interspecific interactions.
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Affiliation(s)
- Xiang Xiong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Hao Liao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Yanfang Xing
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xukun Han
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Wanle Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Wenjie Wan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
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Yang C, Tang W, Sun J, Guo H, Sun S, Miao F, Yang G, Zhao Y, Wang Z, Sun J. Weeds in the Alfalfa Field Decrease Rhizosphere Microbial Diversity and Association Networks in the North China Plain. Front Microbiol 2022; 13:840774. [PMID: 35418969 PMCID: PMC8998637 DOI: 10.3389/fmicb.2022.840774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/07/2022] [Indexed: 11/16/2022] Open
Abstract
The competition between weeds and crops for soil nutrients is affected by soil microorganisms, which drive diverse ecological processes and are critical in maintaining the stability of agroecosystems. However, the effects of plant species identity, particularly between forage and weed, on soil microbial diversity, composition, and association are not well understood. Here, we investigate the soil physicochemical properties and bacterial/fungal communities in an agroecosystem with native alfalfa [Medicago stativa (Ms)] and five common weed species (Digitaria sanguinalis, Echinochloa crusgalli, Acalypha australis, Portulaca oleracea, and Chenopodium album) in the North China Plain. The five weeds had a lower plant carbon content than Ms. while the opposite was true for plant nitrogen and phosphorus concentrations. The Shannon diversity of bacterial and fungal communities of the five weeds were significantly lower than in Ms. Soil pH and PO43−-P were identified as the most important factors in shaping the relative abundances of bacteria (Sphingomonadaceae) and fungi (Pleosporaceae), respectively. Importantly, the weeds greatly inhibited the growth of pathogenic fungi (Nectriaceae and Pleosporaceae). Bacterial co-occurrence networks depended on specific species, indicating that Ms. harbored co-occurrence networks that were more complex than those in the bacterial communities of other weed groups. Our study examines how soil nutrients and the soil microbial community structure of five weed species changed in an Ms. field. This analysis of the microbial ecological network enhances our understanding of the influence of weeds on the soil microbiome in agroecosystems.
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Affiliation(s)
- Chao Yang
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Wei Tang
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Junqi Sun
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
| | - Haipeng Guo
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
| | - Shusheng Sun
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
| | - Fuhong Miao
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Guofeng Yang
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Yiran Zhao
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Zengyu Wang
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Juan Sun
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
- *Correspondence: Juan Sun,
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Ren C, Wang J, Bastida F, Delgado-Baquerizo M, Yang Y, Wang J, Zhong Z, Zhou Z, Zhang S, Guo Y, Zhou S, Wei G, Han X, Yang G, Zhao F. Microbial traits determine soil C emission in response to fresh carbon inputs in forests across biomes. Glob Chang Biol 2022; 28:1516-1528. [PMID: 34807491 DOI: 10.1111/gcb.16004] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Soil priming is a microbial-driven process, which determines key soil-climate feedbacks in response to fresh carbon inputs. Despite its importance, the microbial traits behind this process are largely undetermined. Knowledge of the role of these traits is integral to advance our understanding of how soil microbes regulate carbon (C) emissions in forests, which support the largest soil carbon stocks globally. Using metagenomic sequencing and 13 C-glucose, we provide unprecedented evidence that microbial traits explain a unique portion of the variation in soil priming across forest biomes from tropical to cold temperature regions. We show that microbial functional profiles associated with the degradation of labile C, especially rapid simple sugar metabolism, drive soil priming in different forests. Genes involved in the degradation of lignin and aromatic compounds were negatively associated with priming effects in temperate forests, whereas the highest level of soil priming was associated with β-glucosidase genes in tropical/subtropical forests. Moreover, we reconstructed, for the first time, 42 whole bacterial genomes associated with the soil priming effect and found that these organisms support important gene machinery involved in priming effect. Collectively, our work demonstrates the importance of microbial traits to explain soil priming across forest biomes and suggests that rapid carbon metabolism is responsible for priming effects in forests. This knowledge is important because it advances our understanding on the microbial mechanisms mediating soil-climate feedbacks at a continental scale.
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Affiliation(s)
- Chengjie Ren
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- The Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Yangling, Shaanxi, China
| | - Jieying Wang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi'an, Shaanxi, China
| | - Felipe Bastida
- Department of Soil and Water Conservation, CEBAS-CSIC, Murcia, Spain
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Sevilla, Spain
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jun Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, China
| | - Zekun Zhong
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- The Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Yangling, Shaanxi, China
| | - Zhenghu Zhou
- Center for Ecological Research, Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Shuohong Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- The Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Yangling, Shaanxi, China
| | - Yaoxin Guo
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Sha Zhou
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi'an, Shaanxi, China
| | - Gehong Wei
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinhui Han
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- The Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Yangling, Shaanxi, China
| | - Gaihe Yang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- The Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Yangling, Shaanxi, China
| | - Fazhu Zhao
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi'an, Shaanxi, China
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Jin J, Krohn C, Franks AE, Wang X, Wood JL, Petrovski S, McCaskill M, Batinovic S, Xie Z, Tang C. Elevated atmospheric CO 2 alters the microbial community composition and metabolic potential to mineralize organic phosphorus in the rhizosphere of wheat. Microbiome 2022; 10:12. [PMID: 35074003 PMCID: PMC8785599 DOI: 10.1186/s40168-021-01203-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Understanding how elevated atmospheric CO2 (eCO2) impacts on phosphorus (P) transformation in plant rhizosphere is critical for maintaining ecological sustainability in response to climate change, especially in agricultural systems where soil P availability is low. METHODS This study used rhizoboxes to physically separate rhizosphere regions (plant root-soil interface) into 1.5-mm segments. Wheat plants were grown in rhizoboxes under eCO2 (800 ppm) and ambient CO2 (400 ppm) in two farming soils, Chromosol and Vertosol, supplemented with phytate (organic P). Photosynthetic carbon flow in the plant-soil continuum was traced with 13CO2 labeling. Amplicon sequencing was performed on the rhizosphere-associated microbial community in the root-growth zone, and 1.5 mm and 3 mm away from the root. RESULTS Elevated CO2 accelerated the mineralization of phytate in the rhizosphere zones, which corresponded with increases in plant-derived 13C enrichment and the relative abundances of discreet phylogenetic clades containing Bacteroidetes and Gemmatimonadetes in the bacterial community, and Funneliformis affiliated to arbuscular mycorrhizas in the fungal community. Although the amplicon sequence variants (ASVs) associated the stimulation of phytate mineralization under eCO2 differed between the two soils, these ASVs belonged to the same phyla associated with phytase and phosphatase production. The symbiotic mycorrhizas in the rhizosphere of wheat under eCO2 benefited from increased plant C supply and increased P access from soil. Further supportive evidence was the eCO2-induced increase in the genetic pool expressing the pentose phosphate pathway, which is the central pathway for biosynthesis of RNA/DNA precursors. CONCLUSIONS The results suggested that an increased belowground carbon flow under eCO2 stimulated bacterial growth, changing community composition in favor of phylotypes capable of degrading aromatic P compounds. It is proposed that energy investments by bacteria into anabolic processes increase under eCO2 to level microbial P-use efficiencies and that synergies with symbiotic mycorrhizas further enhance the competition for and mineralization of organic P. Video Abstract.
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Affiliation(s)
- Jian Jin
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscience, La Trobe University, Melbourne Campus, Bundoora, Victoria, 3086, Australia.
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
| | - Christian Krohn
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscience, La Trobe University, Melbourne Campus, Bundoora, Victoria, 3086, Australia
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne Campus, Bundoora, Victoria, 3086, Australia
- Centre for Future Landscapes, La Trobe University, Melbourne Campus, Bundoora, Victoria, 3086, Australia
| | - Xiaojuan Wang
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscience, La Trobe University, Melbourne Campus, Bundoora, Victoria, 3086, Australia
| | - Jennifer L Wood
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne Campus, Bundoora, Victoria, 3086, Australia
- Centre for Future Landscapes, La Trobe University, Melbourne Campus, Bundoora, Victoria, 3086, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne Campus, Bundoora, Victoria, 3086, Australia
| | - Malcolm McCaskill
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Victoria, 3300, Hamilton, Australia
| | - Steven Batinovic
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne Campus, Bundoora, Victoria, 3086, Australia
| | - Zhihuang Xie
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscience, La Trobe University, Melbourne Campus, Bundoora, Victoria, 3086, Australia.
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Bobul'ská L, Espíndola SP, Coelho MA, Ferreira AS. Impact of land use on soil function and bacterial community in the Brazilian savanna. AN ACAD BRAS CIENC 2021; 93:e20201906. [PMID: 34550206 DOI: 10.1590/0001-3765202120201906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/20/2021] [Indexed: 11/21/2022] Open
Abstract
Land use systems have a great impact on soil function and microbial diversity in tropical soils. Our study aimed to evaluate soil biochemical indicators and community composition and to assess the relationship between soil biochemical and microbial indicators and bacterial diversity of three agroecosystems (pine forest, soya and sugarcane) and native Cerrado forest in the Brazilian savanna. Soil biochemical indicators (soil organic matter and enzymes) and high-throughput sequencing of 16S rDNA were performed in two topsoil depths (0-5 cm and 5-10 cm). Soil microbial and enzyme activity showed that agricultural soil usage has a negative impact on soil function compared to native and pine forests. Results also revealed higher enzyme activities in 0-5 cm depth compared to 5-10 cm depth, but enzymatic activities depend on land use systems. Soil bacterial community was affected by land use systems and depth, revealing changes in structure and abundance of bacterial composition. Alpha-diversity indexes were higher in the agricultural systems than in the forests, however they showed a significant negative correlation with most of the studied soil microbial and biochemical indicators. Our research had brought new relevant information about the relationship between the soil biochemical indicators and the bacterial diversity in the Brazilian Cerrado.
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Affiliation(s)
- Lenka Bobul'ská
- University of Prešov in Prešov, Department of Ecology, Faculty of Humanities and Natural Sciences, 17, November 1, Prešov 080 01, Slovakia
| | - Suéllen P Espíndola
- Universidade Federal de Uberlândia, Instituto de Ciências Agrárias, Campus Glória, Bloco CCG, 38410-337 Uberlândia, MG, Brazil
| | - Michelle A Coelho
- Universidade Federal de Uberlândia, Instituto de Ciências Agrárias, Campus Glória, Bloco CCG, 38410-337 Uberlândia, MG, Brazil
| | - Adão S Ferreira
- Universidade Federal de Uberlândia, Instituto de Ciências Agrárias, Campus Glória, Bloco CCG, 38410-337 Uberlândia, MG, Brazil
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Jurkevitch E, Pasternak Z. A walk on the dirt: soil microbial forensics from ecological theory to the crime lab. FEMS Microbiol Rev 2021; 45:5937428. [PMID: 33098291 DOI: 10.1093/femsre/fuaa053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Forensics aims at using physical evidence to solve investigations with science-based principles, thus operating within a theoretical framework. This however is often rather weak, the exception being DNA-based human forensics that is well anchored in theory. Soil is a most commonly encountered, easily and unknowingly transferred evidence but it is seldom employed as soil analyses require extensive expertise. In contrast, comparative analyses of soil bacterial communities using nucleic acid technologies can efficiently and precisely locate the origin of forensic soil traces. However, this application is still in its infancy, and is very rarely used. We posit that understanding the theoretical bases and limitations of their uses is essential for soil microbial forensics to be judiciously implemented. Accordingly, we review the ecological theory and experimental evidence explaining differences between soil microbial communities, i.e. the generation of beta diversity, and propose to integrate a bottom-up approach of interactions at the microscale, reflecting historical contingencies with top-down mechanisms driven by the geographic template, providing a potential explanation as to why bacterial communities map according to soil types. Finally, we delimit the use of soil microbial forensics based on the present technologies and ecological knowledge, and propose possible venues to remove existing bottlenecks.
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Affiliation(s)
- Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zohar Pasternak
- Division of Identification and Forensic Science, Israel Police
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24
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Smercina DN, Bailey VL, Hofmockel KS. Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function. FEMS Microbiol Ecol 2021; 97:6315324. [PMID: 34223869 DOI: 10.1093/femsec/fiab091] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/01/2021] [Indexed: 11/13/2022] Open
Abstract
Soil microorganisms play a key role in driving major biogeochemical cycles and in global responses to climate change. However, understanding and predicting the behavior and function of these microorganisms remains a grand challenge for soil ecology due in part to the microscale complexity of soils. It is becoming increasingly clear that understanding the microbial perspective is vital to accurately predicting global processes. Here, we discuss the microbial perspective including the microbial habitat as it relates to measurement and modeling of ecosystem processes. We argue that clearly defining and quantifying the size, distribution and sphere of influence of microhabitats is crucial to managing microbial activity at the ecosystem scale. This can be achieved using controlled and hierarchical sampling designs. Model microbial systems can provide key data needed to integrate microhabitats into ecosystem models, while adapting soil sampling schemes and statistical methods can allow us to collect microbially-focused data. Quantifying soil processes, like biogeochemical cycles, from a microbial perspective will allow us to more accurately predict soil functions and address long-standing unknowns in soil ecology.
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Affiliation(s)
- Darian N Smercina
- Biological Sciences Division, Earth and Biological Sciences Directorate, 3335 Innovation Blvd, Richland, WA, 99354, USA
| | - Vanessa L Bailey
- Biological Sciences Division, Earth and Biological Sciences Directorate, 3335 Innovation Blvd, Richland, WA, 99354, USA
| | - Kirsten S Hofmockel
- Biological Sciences Division, Earth and Biological Sciences Directorate, 3335 Innovation Blvd, Richland, WA, 99354, USA.,Department of Agronomy, Iowa State University, 716 Farm House Ln, Ames, IA 50011, USA
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Xiong X, Xing Y, He J, Wang L, Shen Z, Chen W, Huang Q. Keystone species determine the "selection mechanism" of multispecies biofilms for bacteria from soil aggregates. Sci Total Environ 2021; 773:145069. [PMID: 33592465 DOI: 10.1016/j.scitotenv.2021.145069] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 01/05/2021] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
Soil aggregates are integral parts of soil structure and play paramount roles in supporting microbial diversity, nutrient cycling and water retention. The formation of multispecies biofilms is a survival strategy for bacterial adaptation to the environment and help microorganisms access more complex nutrient sources via labor sharing, especially in soil aggregates. However, very little is known about the effect of species richness and composition on bacterial multispecies biofilms formation in different size soil aggregates. A random partition design strategy was used to identify the relative importance of bacterial richness and composition in driving multispecies biofilms. The strategy can separate the effects of species richness and composition from the soil aggregates occurring bacterial assemblage. Increasing species richness was found to be always positively correlated with multispecies biofilms productivity for bacteria from the same aggregate fractions. General linear model analysis revealed that species composition contributed more than species richness to forming multispecies biofilms, suggesting that "selection mechanism" plays a more important role than "complementarity mechanism". This "selection mechanism" relies mainly on culturable keystone species that can significantly enhance the formation of multispecies biofilms. The co-occurrence network was investigated to explore whether the culturable keystone species from the random partitions experiment are consistent with the keystone taxa. Four out of 10 culturable keystone species isolated from soil aggregates were matched the keystone taxa. It is concluded that the culturable keystone species determine the multispecies biofilms formation for bacteria residing in soil aggregates. This study provides insights into the role of culturable keystone species in multispecies biofilms. Understanding the formation of multispecies biofilms is fundamental to decipher how microbes interact with each other in soil aggregates. Meanwhile, it will enhance our knowledge of the quorum behavior of complex bacterial communities.
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Affiliation(s)
- Xiang Xiong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanfang Xing
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinzhi He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Wang
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenzhen Shen
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, 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 and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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Behnke GD, Kim N, Zabaloy MC, Riggins CW, Rodriguez-Zas S, Villamil MB. Soil Microbial Indicators within Rotations and Tillage Systems. Microorganisms 2021; 9:1244. [PMID: 34201118 PMCID: PMC8228827 DOI: 10.3390/microorganisms9061244] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/01/2021] [Accepted: 06/06/2021] [Indexed: 01/04/2023] Open
Abstract
Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses.
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Affiliation(s)
- Gevan D. Behnke
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (G.D.B.); (N.K.); (C.W.R.)
| | - Nakian Kim
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (G.D.B.); (N.K.); (C.W.R.)
| | - Maria C. Zabaloy
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS, UNS-CONICET), Departamento de Agronomía, Universidad Nacional del Sur, Bahia Blanca B8000, Argentina;
| | - Chance W. Riggins
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (G.D.B.); (N.K.); (C.W.R.)
| | | | - Maria B. Villamil
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (G.D.B.); (N.K.); (C.W.R.)
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Su H, Xiao Z, Yu K, Zhang Q, Lu C, Wang G, Wang Y, Liang J, Huang W, Huang X, Wei F. High Diversity of β-Glucosidase-Producing Bacteria and Their Genes Associated with Scleractinian Corals. Int J Mol Sci 2021; 22:ijms22073523. [PMID: 33805379 PMCID: PMC8037212 DOI: 10.3390/ijms22073523] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 01/08/2023] Open
Abstract
β-Glucosidase is a microbial cellulose multienzyme that plays an important role in the regulation of the entire cellulose hydrolysis process, which is the rate-limiting step in bacterial carbon cycling in marine environments. Despite its importance in coral reefs, the diversity of β-glucosidase-producing bacteria, their genes, and enzymatic characteristics are poorly understood. In this study, 87 β-glucosidase-producing cultivable bacteria were screened from 6 genera of corals. The isolates were assigned to 21 genera, distributed among three groups: Proteobacteria, Firmicutes, and Actinobacteria. In addition, metagenomics was used to explore the genetic diversity of bacterial β-glucosidase enzymes associated with scleractinian corals, which revealed that these enzymes mainly belong to the glycosidase hydrolase family 3 (GH3). Finally, a novel recombinant β-glucosidase, referred to as Mg9373, encompassing 670 amino acids and a molecular mass of 75.2 kDa, was classified as a member of the GH3 family and successfully expressed and characterized. Mg9373 exhibited excellent tolerance to ethanol, NaCl, and glucose. Collectively, these results suggest that the diversity of β-glucosidase-producing bacteria and genes associated with scleractinian corals is high and novel, indicating great potential for applications in the food industry and agriculture.
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Affiliation(s)
- Hongfei Su
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Zhenlun Xiao
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Kefu Yu
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519080, China
- Correspondence:
| | - Qi Zhang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Chunrong Lu
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Guanghua Wang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Yinghui Wang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Jiayuan Liang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Wen Huang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Xueyong Huang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Fen Wei
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
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Song J, Shen Q, Shi J, Xu J, Brookes PC, Liu X. Changes in microbial community structure due to chronic trace element concentrations in different sizes of soil aggregates. Environ Pollut 2021; 268:115933. [PMID: 33172699 DOI: 10.1016/j.envpol.2020.115933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 09/02/2020] [Accepted: 10/25/2020] [Indexed: 06/11/2023]
Abstract
Studies on the effects of trace elements (TEs) (e.g. Cu, Cd, Zn) on soil microbial communities have provided useful information on the toxicity of TEs to microbes. However, previous studies mainly focused on the effects of TEs on microbial community structure in intact soil, while there are few studies on the impact of TEs on microbial community structure in soil aggregates. In this study, soils previously polluted for 20 years, and now containing low and high TE concentrations derived from, now abandoned, metal smelters were sampled from the surface layer (0-15 cm) of two adjacent Chinese paddy fields. The aim was to determine the effects of TEs on the soil microbial biomass and community structure in different sized soil aggregates. Long-term high TE pollution decreased microbial biomass concentration and species, changed the proportion of bacteria and fungi and decreased the diversity of bacteria in the different sized aggregates. The microbial communities in soil aggregates became clustered with increasing TE concentrations.
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Affiliation(s)
- Jiuwei Song
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, PR China
| | - Qunli Shen
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, PR China
| | - Jiachun Shi
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, PR China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, PR China
| | - Philip C Brookes
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, PR China
| | - Xingmei Liu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, PR China.
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Szoboszlay M, Tebbe CC. Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates. Microbiologyopen 2020; 10:e1144. [PMID: 33369241 PMCID: PMC7884235 DOI: 10.1002/mbo3.1144] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 01/02/2023] Open
Abstract
Sequencing PCR‐amplified gene fragments from metagenomic DNA is a widely applied method for studying the diversity and dynamics of soil microbial communities. Typically, DNA is extracted from 0.25 to 1 g of soil. These amounts, however, neglect the heterogeneity of soil present at the scale of soil aggregates and thus ignore a crucial scale for understanding the structure and functionality of soil microbial communities. Here, we show with a nitrogen‐depleted agricultural soil the impact of reducing the amount of soil used for DNA extraction from 250 mg to approx. 1 mg to access spatial information on the prokaryotic community structure, as indicated by 16S rRNA gene amplicon analyses. Furthermore, we demonstrate that individual aggregates from the same soil differ in their prokaryotic community compositions. The analysis of 16S rRNA gene amplicon sequences from individual soil aggregates allowed us, in contrast to 250 mg soil samples, to construct a co‐occurrence network that provides insight into the structure of microbial associations in the studied soil. Two dense clusters were apparent in the network, one dominated by Thaumarchaeota, known to be capable of ammonium oxidation at low N concentrations, and the other by Acidobacteria subgroup 6, representing an oligotrophic lifestyle to obtain energy from SOC. Overall this study demonstrates that DNA obtained from individual soil aggregates provides new insights into how microbial communities are assembled.
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Affiliation(s)
- Márton Szoboszlay
- Thünen Institut für Biodiversität, Bundesforschungsinstitut für Ländliche Räume, Wald und Fischerei, Braunschweig, Germany
| | - Christoph C Tebbe
- Thünen Institut für Biodiversität, Bundesforschungsinstitut für Ländliche Räume, Wald und Fischerei, Braunschweig, Germany
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Pearman JK, Biessy L, Thomson-Laing G, Waters S, Vandergoes MJ, Howarth JD, Rees A, Moy C, Pochon X, Wood SA. Local factors drive bacterial and microeukaryotic community composition in lake surface sediment collected across an altitudinal gradient. FEMS Microbiol Ecol 2020; 96:5822763. [PMID: 32310266 DOI: 10.1093/femsec/fiaa070] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/18/2020] [Indexed: 01/04/2023] Open
Abstract
Lake surface sediments are dominated by microorganisms that play significant roles in biogeochemical cycling within lakes. There is limited knowledge on the relative importance of local environmental factors and altitude on bacterial and microeukaryotic community richness and composition in lake sediments. In the present study, surface sediment samples were collected from 40 lakes along an altitude gradient (2-1215 m). Microbial communities were characterized using 16S (bacteria) and 18S (microeukaryotes) rRNA gene metabarcoding. Bacterial and microeukaryotic richness were not correlated with altitude but instead to environmental variables (e.g. area of water in the catchment (bacteria: R = -0.43). For both bacteria and microeukaryotes, dissimilarity in the community structure had a higher correlation to combined environmental variables (without altitude) (bacteria: R = 0.53; microeukaryotes: R = 0.55) than altitude alone (bacteria: R = 0.34; microeukaryotes: R = 0.47). Sediment sulfur and productive grassland were important variables in determining the relative abundance of sulfate reducing bacteria. Nitrospira, was positively related to altitude but negatively to water column total organic carbon and the proportion of productive grassland in the catchment. Little overlap in amplicon sequence variants was shown amongst lakes. This has important considerations for management decisions, suggesting that to protect biodiversity, conservation of numerous lakes and lake types is required.
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Affiliation(s)
- John K Pearman
- Cawthron Institute, Coastal and Freshwater Group, 95 Halifax Street East, Nelson, 7010, New Zealand
| | - Laura Biessy
- Cawthron Institute, Coastal and Freshwater Group, 95 Halifax Street East, Nelson, 7010, New Zealand
| | - Georgia Thomson-Laing
- Cawthron Institute, Coastal and Freshwater Group, 95 Halifax Street East, Nelson, 7010, New Zealand
| | - Sean Waters
- Cawthron Institute, Coastal and Freshwater Group, 95 Halifax Street East, Nelson, 7010, New Zealand
| | | | - Jamie D Howarth
- Victoria University of Wellington, School of Geography, Environment and Earth Sciences, PO Box 600, Wellington, New Zealand
| | - Andrew Rees
- Victoria University of Wellington, School of Geography, Environment and Earth Sciences, PO Box 600, Wellington, New Zealand
| | - Chris Moy
- University of Otago, Department of Geology, PO Box 56, Dunedin, 9054, New Zealand
| | - Xavier Pochon
- Cawthron Institute, Coastal and Freshwater Group, 95 Halifax Street East, Nelson, 7010, New Zealand.,University of Auckland, Institute of Marine Science, Private Bag 92019, Auckland, 1142, New Zealand
| | - Susanna A Wood
- Cawthron Institute, Coastal and Freshwater Group, 95 Halifax Street East, Nelson, 7010, New Zealand
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31
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Di L, Li Y, Nie L, Wang S, Kong F. Influence of plant radial oxygen loss in constructed wetland combined with microbial fuel cell on nitrobenzene removal from aqueous solution. J Hazard Mater 2020; 394:122542. [PMID: 32240899 DOI: 10.1016/j.jhazmat.2020.122542] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/09/2020] [Accepted: 03/14/2020] [Indexed: 06/11/2023]
Abstract
This study investigated the effects of radial oxygen loss (ROL) of three different plants on nitrobenzene (NB) wastewater treatment and bioelectricity generation performance in constructed wetland-microbial fuel cell (CW-MFC). ROL and root biomass from wetland plants showed positive effects on NB wastewater compared to unplanted CW-MFC. Scirpus validus exhibited higher tolerance to NB than Typha orientalis and Iris pseudacorus at 20-200 mg/L NB. As NB concentration reached 200 mg/L, the CW-MFC with Scirpus validus had relatively high DO (2.57 ± 0.17 mg/L) and root biomass (16.42 ± 0.18 g/m2), which resulted in the highest power density and voltage (19.5 mW/m2, 590 mV) as well as NB removal efficiency (93.9 %) among four reactors. High-throughput sequencing results suggested that electrochemically active bacteria (EAB) (e.g., Geobacter, Ferruginibacter) and dominant NB-degrading bacteria (e.g., Comamonas, Pseudomonas) could be enhanced by wetland plants, especially in CW-MFC with Scirpus validus. Therefore, Scirpus validus was a good option for simultaneously treating NB wastewater and producing bioelectricity.
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Affiliation(s)
- Liyan Di
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
| | - Yue Li
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
| | - Likai Nie
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
| | - Sen Wang
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China.
| | - Fanlong Kong
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China.
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Yang J, Jiang H, Sun X, Chen J, Xie Z, Dong H. Minerals play key roles in driving prokaryotic and fungal communities in the surface sediments of the Qinghai-Tibetan lakes. FEMS Microbiol Ecol 2020; 96:5780223. [DOI: 10.1093/femsec/fiaa035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 03/02/2020] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
There is limited knowledge of the relative influences of deterministic and stochastic processes on prokaryotic and fungal communities in lake sediments. In this study, we surveyed the prokaryotic and fungal community compositions and their influencing factors in 23 surface sediments from six lakes on the Qinghai-Tibetan Plateau (QTP) with the use of Illumina sequencing. The results showed the distribution of prokaryotic and fungal communities in the studied QTP lake sediments was shaped by different assembly processes, with prokaryotes primarily governed by variable selection and homogenizing dispersal (accounting for 57.9% and 37.3% of the observed variations) and fungi being mainly regulated by variable selection, non-dominant processes and homogenizing dispersal (38.3%, 43.7% and 13.7%, respectively). Regarding the variable selection, mineralogical variables played key roles in shaping prokaryotic and fungal community structures. Collectively, these findings expand current knowledge concerning the influences of deterministic (e.g. variable selection) and stochastic processes (e.g. homogenizing dispersal and non-dominant processes) on the prokaryotic and fungal distribution in the QTP lakes.
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Affiliation(s)
- Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Junsong Chen
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Zhanling Xie
- College of Ecology-Environment Engineering, Qinghai University, Xining, 810016, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, 45056, USA
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Budroni M, Mannazzu I, Zara S, Saba S, Pais A, Zara G. Composition and functional profiling of the microbiota in the casts of Eisenia fetida during vermicomposting of brewers' spent grains. ACTA ACUST UNITED AC 2020; 25:e00439. [PMID: 32140444 DOI: 10.1016/j.btre.2020.e00439] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 01/08/2023]
Abstract
E. fetida microbiota is affected by pH and carbon content of rearing substrates. This is the first report of the microbiota of E. fetida fed with brewers’ spent grains. Brewers’ spent grains induced proliferation of bacterial taxa involved in cellulose degradation and nitrogen cycle. Ammonia and nitrates were assimilated at high rates by the microbiota of E. fetida fed with brewers’ spent grains.
Vermicomposting is a cost-effective biotechnology for the management of organic wastes that relies on the activity of earthworms and their associated microbiota. Here, the microbiotas of the earthworm Eisenia fetida fed with brewers’ spent grains (FBSG), cow manure (FCM) and a mix of brewers’ spent grains/cow manure (FMIX), were identified by high-throughput DNA sequencing (16S rRNA). Bacterial community variance was correlated with the pH and the organic carbon content of the rearing substrates. FBSG microbiota was enriched in Paenibacillaceae, Enterobacteriaceae, Chitinophagaceae and Comamonadaceae. In addition, FBSG microbiota had a predicted higher abundance of genes involved in cellulose degradation as well as in the nitrogen cycle and showed higher utilization of ammonia and nitrate. Results obtained will allow to optimize the vermicomposting of brewers’ spent grains and to evaluate the effect of vermicompost addition on nutrient dynamics in soil.
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Borg Dahl M, Brejnrod AD, Russel J, Sørensen SJ, Schnittler M. Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps. Microb Ecol 2019; 78:764-780. [PMID: 30903202 DOI: 10.1007/s00248-019-01347-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
We used direct DNA amplification from soil extracts to analyze microbial communities from an elevational transect in the German Alps by parallel metabarcoding of bacteria (16S rRNA), fungi (ITS2), and myxomycetes (18S rRNA). For the three microbial groups, 5710, 6133, and 261 operational taxonomic units (OTU) were found. For the latter group, we can relate OTUs to barcodes from fruit bodies sampled over a 4-year period. The alpha diversity of myxomycetes was positively correlated with that of bacteria. Vegetation type was found to be the main explanatory parameter for the community composition of all three groups and a substantial species turnover with elevation was observed. Bacteria and fungi display similar community responses, driven by symbiont species and plant substrate quality. Myxamoebae show a more patchy distribution, though still clearly stratified between taxa, which seems to be a response to both structural properties of the habitat and interaction with specific bacterial and fungal taxa. Finally, we report a high number of myxomycete OTUs not represented in a reference database from fructifications, which might represent novel species.
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Affiliation(s)
- Mathilde Borg Dahl
- Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstrasse 15, 17487, Greifswald, Mecklenburg-Vorpommern, Germany.
| | - Asker Daniel Brejnrod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Russel
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstrasse 15, 17487, Greifswald, Mecklenburg-Vorpommern, Germany
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Meschewski E, Holm N, Sharma BK, Spokas K, Minalt N, Kelly JJ. Pyrolysis biochar has negligible effects on soil greenhouse gas production, microbial communities, plant germination, and initial seedling growth. Chemosphere 2019; 228:565-576. [PMID: 31055071 DOI: 10.1016/j.chemosphere.2019.04.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 04/01/2019] [Accepted: 04/04/2019] [Indexed: 05/21/2023]
Abstract
Biochar has been promoted as a soil amendment that enhances soil quality and agronomic productivity and reduces greenhouse gas production. However, these benefits are not always realized. A major hurdle to the beneficial use of biochar is our limited knowledge regarding the mechanisms directing its effects on soil systems. This project aimed to eliminate some of this uncertainty by examining the biological responses (plant productivity, greenhouse gas production, soil microbial community structure) of a suite of soils (10) to the addition of biochars produced by different processes (pyrolysis, gasification, burning) from a range of feedstocks (corn stalks, hardwood, grass). Results indicated that these three responses were not significantly impacted by the addition of pyrolysis biochars from different feedstocks at 1 and 5% (w/w) addition levels. On the other hand, both an open-air burned corn stalk (5%) and raw corn stalks (1 and 5%) additions did alter the measured soil functionality. For example, the 5% burnt corn stalks addition reduced total above ground plant biomass (∼30%), increased observed N2O production by an order of magnitude, and altered soil bacterial community structure. The bacterial groups that increased in relative abundance in the burnt corn stalks-amended soils included families associated with cellulose decomposition (Chitinophagaceae), plant pathogens (Xanthomonadaceae), and biochar/charcoal-amended media (Gemmatimonadetes). In contrast, the abundance of these bacterial groups was not impacted by the pyrolysis biochars. Therefore, this research suggests that pyrolysis biochar represents a stabilized form of carbon that is resistant to microbial mineralization and has negligible effects on soil biological responses.
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Affiliation(s)
- Elizabeth Meschewski
- Illinois Sustainable Technology Center, Prairie Research Institute, University of Illinois at Urbana-Champaign, USA.
| | - Nancy Holm
- Illinois Sustainable Technology Center, Prairie Research Institute, University of Illinois at Urbana-Champaign, USA
| | - Brajendra K Sharma
- Illinois Sustainable Technology Center, Prairie Research Institute, University of Illinois at Urbana-Champaign, USA
| | - Kurt Spokas
- Agricultural Research Service, United States Department of Agriculture (USDA), USA
| | - Nicole Minalt
- Department of Biology, Loyola University Chicago, USA
| | - John J Kelly
- Department of Biology, Loyola University Chicago, USA
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Ma L, Zhao B, Guo Z, Wang D, Li D, Xu J, Li Z, Zhang J. Divergent responses of bacterial activity, structure, and co-occurrence patterns to long-term unbalanced fertilization without nitrogen, phosphorus, or potassium in a cultivated vertisol. Environ Sci Pollut Res Int 2019; 26:12741-12754. [PMID: 30879236 DOI: 10.1007/s11356-019-04839-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
Unbalanced fertilization lacking nitrogen (N), phosphorus (P), or potassium (K) is a worldwide phenomenon; however, whether they affect bacterial community composition and intraspecific interactions in a similar pattern and how they affect bacterial activity are not systematically compared. Soils under different kinds of unbalanced fertilization in a 21-year field experiment were collected to investigate the variation in dehydrogenase activity (DHA), bacterial community diversity, structure, composition, and possible interactions. Compared to the balanced fertilization of NPK, the DHA from unbalanced fertilization of NP, PK, and NK was 8.70, 11.59, and 14.17% lower, respectively, and from the unfertilized treatment (Nil) was 13.41% lower; however, the Shannon index from NP, PK, and Nil was 4.48-7.21% higher and from NK was 3.95% lower. Based on principal coordinate analyses (PCoA), bacterial community structure was separated by N application or not along PCo1 and was further separated by P application or not along PCo2, indicating a more influence by N deficiency. Moreover, the structure was mainly determined by soil pH, soil organic carbon (SOC), and total phosphorus (TP). The network complexity using co-occurrence analysis followed the order NP > NPK > PK > NK > Nil, indicating a more influence by P deficiency on intraspecific interactions. Structural equation modeling (SEM) revealed that the reduced DHA in NP was mainly regulated by the decreased SOC and increased Shannon index, in PK by the decreased SOC and increased Shannon index and pH, and in NK by the decreased SOC and TP and increased PCo2. The significantly lower abundance of Bacteroidetes and Chitinophagaceae in NK may also contribute to the reduced DHA. Our results imply that N deficiency had the greatest impact on bacterial community structure and composition, P deficiency had the greatest impact on network construction and bacterial activity, and K deficiency has minimal effect. Our results also suggest that main factors regulating the variation in soil functions may vary among different nutrient deficiencies.
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Affiliation(s)
- Lei Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingzi Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Zhibin Guo
- Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Daozhong Wang
- Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Dandan Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jisheng Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zengqiang Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
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Taubert M, Stähly J, Kolb S, Küsel K. Divergent microbial communities in groundwater and overlying soils exhibit functional redundancy for plant-polysaccharide degradation. PLoS One 2019; 14:e0212937. [PMID: 30865693 DOI: 10.1371/journal.pone.0212937] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/12/2019] [Indexed: 11/19/2022] Open
Abstract
Light driven primary production by plants is the main source of biomass in terrestrial ecosystems. But also in subsurface habitats like aquifers, life is fueled largely by this plant-derived biomass. Here, we investigate the degradation of plant-derived polysaccharides in a groundwater microbiome to identify the microbial key players involved, and compare them to those from soil of the groundwater recharge area. We quantified the activities of enzymes degrading the abundant plant polymers starch, cellulose and hemicellulose in oligotrophic groundwater samples, despite the low cell numbers present. Normalized to 16S rRNA gene copy numbers, these activities were only one order of magnitude lower than in soil. Stimulation of the groundwater microbiome with either starch or cellulose and hemicellulose led to changes of the enzymatic activity ratios, indicating autochthonous production of enzymes in response to the plant polymers. Furthermore, DNA stable isotope probing with 13C labelled plant polymers allowed us to identify microbes involved in the degradation of these compounds. In (hemi)cellulose microcosms, Bacteroidia and Candidatus Parcubacteria were active, while the active community in starch microcosms mostly comprised Candidatus Saccharibacteria, Cytophagia, and Actinobacteria. Not a single one of the active OTUs was also found to be labelled in soil microcosms. This indicates that the degradation of plant-derived polysaccharides in groundwater is driven by organisms completely distinct from those active in soil. The involvement of members of the candidate phyla Cand. Parcubacteria and Cand. Saccharibacteria, organisms known to be abundant in groundwater, in plant-derived organic matter degradation might strongly impact subsurface carbon cycling.
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Maza F, Maldonado J, Vásquez-Dean J, Mandakovic D, Gaete A, Cambiazo V, González M. Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability. Front Bioeng Biotechnol 2019; 7:10. [PMID: 30805333 PMCID: PMC6371850 DOI: 10.3389/fbioe.2019.00010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/16/2019] [Indexed: 11/13/2022] Open
Abstract
The Atacama Desert is a highly complex, extreme ecosystem which harbors microorganisms remarkable for their biotechnological potential. Here, a soil bacterial prospection was carried out in the high Altiplano region of the Atacama Desert (>3,800 m above sea level; m a.s.l.), where direct anthropogenic interference is minimal. We studied: (1) soil bacterial community composition using high-throughput sequencing of the 16S rRNA gene and (2) bacterial culturability, by using a soil extract medium (SEM) under a factorial design of three factors: temperature (15 and 30°C), nutrient content (high and low nutrient disposal) and oxygen availability (presence and absence). A total of 4,775 OTUs were identified and a total of 101 isolates were selected for 16S rRNA sequencing, 82 of them corresponded to unique or non-redundant sequences. To expand our view of the Altiplano landscape and to obtain a better representation of its microbiome, we complemented our Operational Taxonomic Units (OTUs) and isolate collection with data from other previous data from our group and obtained a merged set of OTUs and isolates that we used to perform our study. Taxonomic comparisons between culturable microbiota and metabarcoding data showed an overrepresentation of the phylum Firmicutes (44% of isolates vs. 2% of OTUs) and an underrepresentation of Proteobacteria (8% of isolates vs. 36% of OTUs). Within the Next Generation Sequencing (NGS) results, 33% of the OTUs were unknown up to genus, revealing an important proportion of putative new species in this environment. Biochemical characterization and analysis extracted from the literature indicated that an important number of our isolates had biotechnological potential. Also, by comparing our results with similar studies on other deserts, the Altiplano highland was most similar to a cold arid desert. In summary, our study contributes to expand the knowledge of soil bacterial communities in the Atacama Desert and complements the pipeline to isolate selective bacteria that could represent new potential biotechnological resources.
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Affiliation(s)
- Felipe Maza
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation, Santiago, Chile
| | - Jonathan Maldonado
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation, Santiago, Chile
| | - Javiera Vásquez-Dean
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Dinka Mandakovic
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation, Santiago, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation, Santiago, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation, Santiago, Chile
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39
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Pang M, Xie X, Bao H, Sun L, He T, Zhao H, Zhou Y, Zhang L, Zhang H, Wei R, Xie K, Wang R. Insights Into the Bovine Milk Microbiota in Dairy Farms With Different Incidence Rates of Subclinical Mastitis. Front Microbiol 2018; 9:2379. [PMID: 30459717 PMCID: PMC6232673 DOI: 10.3389/fmicb.2018.02379] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/18/2018] [Indexed: 12/18/2022] Open
Abstract
Bovine mastitis continues to be a complex disease associated with significant economic loss in dairy industries worldwide. The incidence rate of subclinical mastitis (IRSCM) can show substantial variation among different farms; however, the milk microbiota, which have a direct influence on bovine mammary gland health, have never been associated with the IRSCM. Here, we aimed to use high-throughput DNA sequencing to describe the milk microbiota from two dairy farms with different IRSCMs and to identify the predominant mastitis pathogens along with commensal or potential beneficial bacteria. Our study showed that Klebsiella, Escherichia-Shigella, and Streptococcus were the mastitis-causing pathogens in farm A (with a lower IRSCM), while Streptococcus and Corynebacterium were the mastitis-causing pathogens in farm B (with a higher IRSCM). The relative abundance of all pathogens in farm B (22.12%) was higher than that in farm A (9.82%). However, the genus Bacillus was more prevalent in farm A. These results may be helpful for explaining the lower IRSCM in farm A. Additionally, the gut-associated genera Prevotella, Ruminococcus, Bacteroides, Rikenella, and Alistipes were prevalent in all milk samples, suggesting gut bacteria can be one of the predominant microbial contamination in milk. Moreover, Listeria monocytogenes (a foodborne pathogen) was found to be prevalent in farm A, even though it had a lower IRSCM. Overall, our study showed complex diversity between the milk microbiota in dairy farms with different IRSCMs. This suggests that variation in IRSCMs may not only be determined by the heterogeneity and prevalence of mastitis-causing pathogens but also be associated with potential beneficial bacteria. In the future, milk microbiota should be considered in bovine mammary gland health management. This would be helpful for both the establishment of a targeted mastitis control system and the control of the safety and quality of dairy products.
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Affiliation(s)
- Maoda Pang
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xing Xie
- Key Laboratory of Veterinary Biological Engineering and Technology, Institute of Veterinary Medicine, Ministry of Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hongduo Bao
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lichang Sun
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tao He
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hang Zhao
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yan Zhou
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lili Zhang
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hui Zhang
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ruicheng Wei
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Kaizhou Xie
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ran Wang
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Farhat M, Shaheed RA, Al-Ali HH, Al-Ghamdi AS, Al-Hamaqi GM, Maan HS, Al-Mahfoodh ZA, Al-Seba HZ. Legionella confirmation in cooling tower water. Comparison of culture, real-time PCR and next generation sequencing. Saudi Med J 2018; 39:137-141. [PMID: 29436561 PMCID: PMC5885089 DOI: 10.15537/smj.2018.2.21587] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Objectives: To investigate the presence of Legionella spp in cooling tower water. Legionella proliferation in cooling tower water has serious public health implications as it can be transmitted to humans via aerosols and cause Legionnaires’ disease. Methods: Samples of cooling tower water were collected from King Fahd Hospital of the University (KFHU) (Imam Abdulrahman Bin Faisal University, 2015/2016). The water samples were analyzed by a standard Legionella culture method, real-time polymerase chain reaction (RT-PCR), and 16S rRNA next-generation sequencing. In addition, the bacterial community composition was evaluated. Results: All samples were negative by conventional Legionella culture. In contrast, all water samples yielded positive results by real-time PCR (105 to 106 GU/L). The results of 16S rRNA next generation sequencing showed high similarity and reproducibility among the water samples. The majority of sequences were Alpha-, Beta-, and Gamma-proteobacteria, and Legionella was the predominant genus. The hydrogen-oxidizing gram-negative bacterium Hydrogenophaga was present at high abundance, indicating high metabolic activity. Sphingopyxis, which is known for its resistance to antimicrobials and as a pioneer in biofilm formation, was also detected. Conclusion: Our findings indicate that monitoring of Legionella in cooling tower water would be enhanced by use of both conventional culturing and molecular methods.
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Affiliation(s)
- Maha Farhat
- Department of Biochemistry, Imam Abdulrahman Bin Faisal University, Dammam, Kindgdom of Saudi Arabia. E-mail.
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Mandakovic D, Maldonado J, Pulgar R, Cabrera P, Gaete A, Urtuvia V, Seeger M, Cambiazo V, González M. Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert. Extremophiles 2018. [PMID: 29687212 DOI: 10.1007/s00792-018-1027-6/figures/3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
As a consequence of the severe climatic change affecting our entire world, many lakes in the Andes Cordillera are likely to disappear within a few decades. One of these lakes is Lejía Lake, located in the central Atacama Desert. The objectives of this study were: (1) to characterize the bacterial community from Lejía Lake shore soil (LLS) using 16S rRNA sequencing and (2) to test a culture-based approach using a soil extract medium (SEM) to recover soil bacteria. This extreme ecosystem was dominated by three phyla: Bacteroidetes, Proteobacteria, and Firmicutes with 29.2, 28.2 and 28.1% of the relative abundance, respectively. Using SEM, we recovered 7.4% of the operational taxonomic units from LLS, all of which belonged to the same three dominant phyla from LLS (6.9% of Bacteroidetes, 77.6% of Proteobacteria, and 15.3% of Firmicutes). In addition, we used SEM to recover isolates from LLS and supplemented the culture medium with increasing salt concentrations to isolate microbial representatives of salt tolerance (Halomonas spp.). The results of this study complement the list of microbial taxa diversity from the Atacama Desert and assess a pipeline to isolate selective bacteria that could represent useful elements for biotechnological approaches.
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Affiliation(s)
- Dinka Mandakovic
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Jonathan Maldonado
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Rodrigo Pulgar
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Pablo Cabrera
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Viviana Urtuvia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Center for Nanotechnology, Systems Biology and Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España, 1680, Valparaiso, Chile
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil, 2147, Valparaiso, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Center for Nanotechnology, Systems Biology and Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España, 1680, Valparaiso, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile.
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.
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42
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Zhu FP, Duan JL, Yuan XZ, Shi XS, Han ZL, Wang SG. Hydrolysis, adsorption, and biodegradation of bensulfuron methyl under methanogenic conditions. Chemosphere 2018; 199:138-146. [PMID: 29433027 DOI: 10.1016/j.chemosphere.2018.01.149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 01/23/2018] [Accepted: 01/28/2018] [Indexed: 06/08/2023]
Abstract
Bensulfuron methyl (BSM), one of the most widely used herbicides in paddy soils, is frequently detected in natural and artificial aquatic systems. However, BSM transformation under methanogenic conditions has not been given sufficient attention. In this study, BSM elimination and transformation by anaerobic enrichment cultures were investigated. The results showed that BSM can be mineralized to methane through hydrolysis, adsorption, and biodegradation under a methanogenic environment. The adsorption led to protein static quenching in the extracellular polymeric substances (EPSs) of the enrichment cultures. Specifically, BSM mainly reacted with the amine, amide, amino acid, and amino sugar functional groups in proteins. BSM hydrolysis and biodegradation occurred through the breakage of the sulfonylurea bridge and sulfonyl amide linkage. The cleavage of the sulfonylurea bridge occurred in both hydrolysis and biodegradation, while the cleavage of the sulfonyl amide linkage only occurred in hydrolysis. These results elucidated the complex transformation of BSM under methanogenic conditions, which will advance the studies on sulfonylurea herbicide biotransformation and hazard assessment in the environment.
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Affiliation(s)
- Fan-Ping Zhu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, Shandong Province 250100, PR China
| | - Jian-Lu Duan
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Xian-Zheng Yuan
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, Shandong Province 250100, PR China.
| | - Xiao-Shuang Shi
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Zhen-Lian Han
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Shu-Guang Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, Shandong Province 250100, PR China.
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Mandakovic D, Maldonado J, Pulgar R, Cabrera P, Gaete A, Urtuvia V, Seeger M, Cambiazo V, González M. Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert. Extremophiles 2018; 22:665-673. [PMID: 29687212 DOI: 10.1007/s00792-018-1027-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 04/13/2018] [Indexed: 12/31/2022]
Abstract
As a consequence of the severe climatic change affecting our entire world, many lakes in the Andes Cordillera are likely to disappear within a few decades. One of these lakes is Lejía Lake, located in the central Atacama Desert. The objectives of this study were: (1) to characterize the bacterial community from Lejía Lake shore soil (LLS) using 16S rRNA sequencing and (2) to test a culture-based approach using a soil extract medium (SEM) to recover soil bacteria. This extreme ecosystem was dominated by three phyla: Bacteroidetes, Proteobacteria, and Firmicutes with 29.2, 28.2 and 28.1% of the relative abundance, respectively. Using SEM, we recovered 7.4% of the operational taxonomic units from LLS, all of which belonged to the same three dominant phyla from LLS (6.9% of Bacteroidetes, 77.6% of Proteobacteria, and 15.3% of Firmicutes). In addition, we used SEM to recover isolates from LLS and supplemented the culture medium with increasing salt concentrations to isolate microbial representatives of salt tolerance (Halomonas spp.). The results of this study complement the list of microbial taxa diversity from the Atacama Desert and assess a pipeline to isolate selective bacteria that could represent useful elements for biotechnological approaches.
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Affiliation(s)
- Dinka Mandakovic
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Jonathan Maldonado
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Rodrigo Pulgar
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Pablo Cabrera
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Viviana Urtuvia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Center for Nanotechnology, Systems Biology and Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España, 1680, Valparaiso, Chile
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil, 2147, Valparaiso, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Center for Nanotechnology, Systems Biology and Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España, 1680, Valparaiso, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile.
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.
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Ricketts M, Flower C, Knight K, Gonzalez-meler M. Evidence of Ash Tree (Fraxinus spp.) Specific Associations with Soil Bacterial Community Structure and Functional Capacity. Forests 2018; 9:187. [DOI: 10.3390/f9040187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Rodrigues RR, Rodgers NC, Wu X, Williams MA. COREMIC: a web-tool to search for a niche associated CORE MICrobiome. PeerJ 2018; 6:e4395. [PMID: 29473009 PMCID: PMC5816963 DOI: 10.7717/peerj.4395] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/30/2018] [Indexed: 02/01/2023] Open
Abstract
Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool “COREMIC” meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com or http://core-mic.com), developed using Google App Engine, to help in the process of database mining to identify the “core microbiome” associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (five environments), and conservative statistical criteria (presence in more than 90% samples and FDR q-val <0.05% for Fisher’s exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using currently available databases and a unique freely available software.
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Affiliation(s)
- Richard R Rodrigues
- Interdisciplinary Ph.D. Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.,Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, United States of America
| | - Nyle C Rodgers
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Xiaowei Wu
- Department of Statistics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Mark A Williams
- Interdisciplinary Ph.D. Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.,School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
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Nguyen STC, Freund HL, Kasanjian J, Berlemont R. Function, distribution, and annotation of characterized cellulases, xylanases, and chitinases from CAZy. Appl Microbiol Biotechnol 2018; 102:1629-1637. [PMID: 29359269 DOI: 10.1007/s00253-018-8778-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/06/2018] [Accepted: 01/09/2018] [Indexed: 11/30/2022]
Abstract
The enzymatic deconstruction of structural polysaccharides, which relies on the production of specific glycoside hydrolases (GHs), is an essential process across environments. Over the past few decades, researchers studying the diversity and evolution of these enzymes have isolated and biochemically characterized thousands of these proteins. The carbohydrate-active enzymes database (CAZy) lists these proteins and provides some metadata. Here, the sequences and metadata of characterized sequences derived from GH families associated with the deconstruction of cellulose, xylan, and chitin were collected and discussed. First, although few polyspecific enzymes are identified, characterized GH families are mostly monospecific. Next, the taxonomic distribution of characterized GH mirrors the distribution of identified sequences in sequenced genomes. This provides a rationale for connecting the identification of GH sequences to specific reactions or lineages. Finally, we tested the annotation of the characterized GHs using HMM scan and the protein families database (Pfam). The vast majority of GHs targeting cellulose, xylan, and chitin can be identified using this publicly accessible approach.
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Affiliation(s)
- Stanley T C Nguyen
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Hannah L Freund
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Joshua Kasanjian
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Renaud Berlemont
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA.
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Avershina E, Slangsvold S, Simpson MR, Storrø O, Johnsen R, Øien T, Rudi K. Diversity of vaginal microbiota increases by the time of labor onset. Sci Rep 2017; 7:17558. [PMID: 29242550 PMCID: PMC5730599 DOI: 10.1038/s41598-017-17972-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/04/2017] [Indexed: 01/09/2023] Open
Abstract
Vaginal microbiota is an important early source of bacterial colonization for newborns. However, only a few small studies have investigated the composition of vaginal microbiota during labor. In this work, we analyzed vaginal swabs collected at 36 weeks gestation and at the onset of labor from 256 women participating in a randomized placebo-controlled study of probiotic supplementation for the prevention of atopic dermatitis in offspring. Although individuals' vaginal microbiota was stable over time, several bacterial families, which are characteristic of mixed community state type (CST) IV, were overrepresented in vaginal swabs sampled at labor. Alpha-diversity also tended to increase by between 36 weeks gestation and the onset of birth. In the majority of women, CST remained the same throughout the study. Among the women who switched their vaginal microbiota from one CST to another, approximately half shifted towards CST IV. Although CST IV is often associated with bacterial vaginosis, which in turn may lead to preterm birth, in our cohort this shift was not associated with self-reported vaginosis, preterm delivery or birthweight. Probiotic consumption did not alter vaginal microbiota.
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Affiliation(s)
- Ekaterina Avershina
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway.
| | - Silje Slangsvold
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | - Melanie Rae Simpson
- Department of Public Health and Nursing, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Ola Storrø
- Department of Public Health and Nursing, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Roar Johnsen
- Department of Public Health and Nursing, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Torbjørn Øien
- Department of Public Health and Nursing, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
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Probandt D, Eickhorst T, Ellrott A, Amann R, Knittel K. Microbial life on a sand grain: from bulk sediment to single grains. ISME J 2017; 12:623-633. [PMID: 29192905 PMCID: PMC5776476 DOI: 10.1038/ismej.2017.197] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/04/2017] [Accepted: 10/09/2017] [Indexed: 11/09/2022]
Abstract
Globally, marine surface sediments constitute a habitat for estimated 1.7 × 1028 prokaryotes. For benthic microbial community analysis, usually, several grams of sediment are processed. In this study, we made the step from bulk sediments to single sand grains to address the microbial community directly in its micro-habitat: the individual bacterial diversity on 17 sand grains was analyzed by 16S ribosomal RNA gene sequencing and visualized on sand grains using catalyzed reporter deposition fluorescence in situ hybridization. In all, 104-105 cells were present on grains from 202 to 635 μm diameter. Colonization was patchy, with exposed areas largely devoid of any epi-growth (mean cell-cell distance 4.5±5.9 μm) and protected areas more densely populated (0.5±0.7 μm). Mean cell-cell distances were 100-fold shorter compared with the water column. In general, growth occurred in monolayers. Each sand grain harbors a highly diverse bacterial community as shown by several thousand species-level operational taxonomic units (OTU)0.97. Only 4-8 single grains are needed to cover 50% of OTU0.97 richness found in bulk sediment. Although bacterial communities differed between sand grains, a core community accounting for >50% of all cells was present on each sand grain. The communities between sediment grains are more similar than between soil macroaggregates.
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Affiliation(s)
- David Probandt
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany
| | - Thilo Eickhorst
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany.,University of Bremen, Faculty 2 (Biology/Chemistry), Bremen, Germany
| | - Andreas Ellrott
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany
| | - Katrin Knittel
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany
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49
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Tan W, Wang G, Huang C, Gao R, Xi B, Zhu B. Physico-chemical protection, rather than biochemical composition, governs the responses of soil organic carbon decomposition to nitrogen addition in a temperate agroecosystem. Sci Total Environ 2017; 598:282-288. [PMID: 28445825 DOI: 10.1016/j.scitotenv.2017.04.143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/19/2017] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Abstract
The heterogeneous responses of soil organic carbon (SOC) decomposition in different soil fractions to nitrogen (N) addition remain elusive. In this study, turnover rates of SOC in different aggregate fractions were quantified based on changes in δ13C following the conversion of C3 to C4 vegetation in a temperate agroecosystem. The turnover of both total organic matter and specific organic compound classes within each aggregate fraction was inhibited by N addition. Moreover, the intensity of inhibition increases with decreasing aggregate size and increasing N addition level, but does not vary among chemical compound classes within each aggregate fraction. Overall, the response of SOC decomposition to N addition is dependent on the physico-chemical protection of SOC by aggregates and minerals, rather than the biochemical composition of organic substrates. The results of this study could help to understand the fate of SOC in the context of increasing N deposition.
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Affiliation(s)
- Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Guoan Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Caihong Huang
- State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Rutai Gao
- State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Biao Zhu
- College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China.
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50
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Medeiros JD, Leite LR, Pylro VS, Oliveira FS, Almeida VM, Fernandes GR, Salim ACM, Araújo FMG, Volpini AC, Oliveira G, Cuadros-Orellana S. Single-cell sequencing unveils the lifestyle and CRISPR-based population history of Hydrotalea
sp. in acid mine drainage. Mol Ecol 2017; 26:5541-5551. [DOI: 10.1111/mec.14294] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/21/2017] [Accepted: 07/27/2017] [Indexed: 01/20/2023]
Affiliation(s)
- J. D. Medeiros
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
- Institute of Biological Sciences; Federal University of Minas Gerais; UFMG; Belo Horizonte MG Brazil
| | - L. R. Leite
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
- Institute of Biological Sciences; Federal University of Minas Gerais; UFMG; Belo Horizonte MG Brazil
| | - V. S. Pylro
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
- Department of Soil Science; “Luiz de Queiroz” College of Agriculture; University of São Paulo; ESALQ/USP; Piracicaba SP Brazil
| | - F. S. Oliveira
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
- Institute of Biological Sciences; Federal University of Minas Gerais; UFMG; Belo Horizonte MG Brazil
| | - V. M. Almeida
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
- Institute of Biological Sciences; Federal University of Minas Gerais; UFMG; Belo Horizonte MG Brazil
| | - G. R. Fernandes
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
| | - A. C. M. Salim
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
| | - F. M. G. Araújo
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
| | - A. C. Volpini
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
| | - G. Oliveira
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
- Vale Institute of Technology - Sustainable Development; Belém PA Brazil
| | - S. Cuadros-Orellana
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
- Centro de Biotecnología de los Recursos Naturales; Facultad de Ciencias Agrarias y Forestales; Universidad Católica del Maule; Talca Chile
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