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1.
Environ Sci Technol ; 55(11): 7445-7455, 2021 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-33977709

RESUMO

Earthworms are capable of redistributing bacteria and antibiotic resistance genes (ARGs) through soil profiles. However, our understanding of the earthworm gut microbiome and its interaction with the antibiotic resistome is still lacking. Here, we characterized the earthworm gut and soil microbiome and antibiotic resistome in natural and agricultural ecosystems at a national scale, and microcosm studies and field experiments were also employed to test the potential role of earthworms in dynamics of soil ARGs. The diversity and structure of bacterial communities were different between the earthworm gut and soil. A significant correlation between bacterial community dissimilarity and spatial distance between sites was identified in the earthworm gut. The earthworm gut consistently had lower ARGs than the surrounding soil. A significant reduction in the relative abundance of mobile genetic elements and dominant bacterial phylotypes that are the likely hosts of ARGs was observed in the earthworm gut compared to the surrounding soil, which might contribute to the decrease of ARGs in the earthworm gut. The microcosm studies and field experiments further confirmed that the presence of earthworms significantly reduced the number and abundance of ARGs in soils. Our study implies that earthworm-based bioremediation may be a method to reduce risks associated with the presence of ARGs in soils.

2.
Water Res ; 198: 117139, 2021 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-33895591

RESUMO

Glacier-fed aquatic ecosystems provide habitats for diverse and active bacterial communities. However, the environmental vulnerabilities of co-existing water and sediment bacterial communities in these ecosystems remain unclear. Here, 16S rRNA gene sequencing was used to investigate co-existing bacterial communities in paired water and sediment samples from multiple rivers and lakes that are mainly fed by glaciers from the southeast Tibetan Plateau. Overall, the bacterial communities were dissimilar between the water and sediment, which indicated that there were limited interactions between them. Bacterial diversity was greatest in the sediments, where it was mainly driven by changes in nitrogen compounds and pH. Meanwhile water bacterial diversity was more susceptible to evapotranspiration, elevation, and mean annual temperature. Water samples contained higher proportions of Proteobacteria and Bacteroidetes, while sediment harbored higher proportions of Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Cyanobacteria, and Gemmatimonadetes. Bacterial community composition was significantly correlated with mean annual precipitation in water, but with nitrogen compounds in sediment. The co-occurrence network of water included more keystone species (e.g., CL500-29 marine group, Nocardioides spp., and Bacillus spp.) than the sediment network. These keystone species showed stronger phylogenetic signals than the species in the modular structures. Further, ecological clusters within the networks suggested that there were contrasting environmental vulnerabilities and preferences between water and sediment communities. These findings demonstrated that co-existing water and sediment bacterial communities and ecological clusters were shaped by contrasting environmental factors. This work provides a basis for understanding the importance of bacterial communities in maintaining glacier-fed aquatic ecosystems. Further, the results provide new perspectives for water resource management and water conservation in changing environments.


Assuntos
Ecossistema , Camada de Gelo , Sedimentos Geológicos , Filogenia , RNA Ribossômico 16S/genética , Água
3.
New Phytol ; 2021 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-33864276

RESUMO

Despite their extent and socio-ecological importance, a comprehensive biogeographical synthesis of drylands is lacking. Here we synthesize the biogeography of key organisms (vascular and nonvascular vegetation and soil microorganisms), attributes (functional traits, spatial patterns, plant-plant and plant-soil interactions) and processes (productivity and land cover) across global drylands. These areas have a long evolutionary history, are centers of diversification for many plant lineages and include important plant diversity hotspots. This diversity captures a strikingly high portion of the variation in leaf functional diversity observed globally. Part of this functional diversity is associated with the large variation in response and effect traits in the shrubs encroaching dryland grasslands. Aridity and its interplay with the traits of interacting plant species largely shape biogeographical patterns in plant-plant and plant-soil interactions, and in plant spatial patterns. Aridity also drives the composition of biocrust communities and vegetation productivity, which shows large geographical variation. We finish our review by discussing major research gaps, which include: studying regular vegetation spatial patterns; establishing large-scale plant and biocrust field surveys assessing individual-level trait measurements; knowing whether the impacts of plant-plant and plant-soil interactions on biodiversity are predictable; and assessing how elevated CO2 modulates future aridity conditions and plant productivity.

4.
New Phytol ; 2021 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-33914920

RESUMO

Lichens play crucial roles in sustaining the functioning of terrestrial ecosystems; however, the diversity and ecological factors associated with lichenised soil fungi remain poorly understood. To address this knowledge gap, we used a global field survey including information on fungal sequences of topsoils from 235 terrestrial ecosystems. We identified 880 lichenised fungal phylotypes across nine biomes ranging from deserts to tropical forests. The diversity and proportion of lichenised soil fungi peaked in shrublands and dry grasslands. Aridity index, plant cover and soil pH were the most important factors associated with the distribution of lichenised soil fungi. Furthermore, we identified Endocarpon, Verrucaria and Rinodina as some of the most dominant lichenised genera across the globe, and they had similar environmental preferences to the lichenised fungal community. In addition, precipitation seasonality and mean diurnal temperature range were also important in predicting the proportion of these dominant genera. Using this information, we were able to create the first global maps of the richness and the proportion of dominant genera of lichenised fungi. This work provides new insight into the global distribution and ecological preferences of lichenised soil fungi, and supports their dominance in drylands across the globe.

5.
J Proteomics ; 237: 104147, 2021 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-33582288

RESUMO

We lack a predictive understanding of the environmental drivers determining the structure and function of archaeal communities as well as the proteome associated with these important soil organisms. Here, we characterized the structure (by 16S rRNA gene sequencing) and function (by metaproteomics) of archaea from 32 soil samples across terrestrial ecosystems with contrasting climate and vegetation types. Our multi-"omics" approach unveiled that genes from Nitrosophaerales and Thermoplasmata dominated soils collected from four continents, and that archaea comprise 2.3 ± 0.3% of microbial proteins in these soils. Aridity positively correlated with the proportion of Nitrosophaerales genes and the number of archaeal proteins. The interaction of climate x vegetation shaped the functional profile of the archaeal community. Our study provides novel insights into the structure and function of soil archaea across climates, and highlights that these communities may be influenced by increasing global aridity.

6.
ISME J ; 2021 Feb 09.
Artigo em Inglês | MEDLINE | ID: mdl-33564112

RESUMO

The relationship between biodiversity and biomass has been a long standing debate in ecology. Soil biodiversity and biomass are essential drivers of ecosystem functions. However, unlike plant communities, little is known about how the diversity and biomass of soil microbial communities are interlinked across globally distributed biomes, and how variations in this relationship influence ecosystem function. To fill this knowledge gap, we conducted a field survey across global biomes, with contrasting vegetation and climate types. We show that soil carbon (C) content is associated to the microbial diversity-biomass relationship and ratio in soils across global biomes. This ratio provides an integrative index to identify those locations on Earth wherein diversity is much higher compared with biomass and vice versa. The soil microbial diversity-to-biomass ratio peaks in arid environments with low C content, and is very low in C-rich cold environments. Our study further advances that the reductions in soil C content associated with land use intensification and climate change could cause dramatic shifts in the microbial diversity-biomass ratio, with potential consequences for broad soil processes.

7.
Environ Int ; 151: 106438, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33621916

RESUMO

The colossal project of mapping the microbiome on Earth is rapidly advancing, with a focus on individual microbial groups. However, a global assessment of the associations between predatory protists and their bacterial prey is still missing at a cross-ecosystem level. This knowledge is critical to better understand the importance of top-down links in structuring microbiomes. Here, we examined 38 sequence-based datasets of paired bacterial and protistan taxa, covering 3,178 samples from diverse habitats including freshwater, marine and soils. We show that community profiles of protists and bacteria strongly correlated across and within habitats, with trophic microbiome structures fundamentally differing across habitats. Soils hosted the most heterogenous and diverse microbiomes. Protist communities were dominated by predators in soils and phototrophs in aquatic environments. This led to changes in the ratio of total protists to bacteria richness, which was highest in marine, while that of predatory protists to bacteria was highest in soils. Taxon richness and relative abundance of predatory protists positively correlated with bacterial richness in marine habitats. These links differed between soils, predatory protist richness and the relative abundance of predatory protists positively correlated with bacterial richness in forest and grassland soils, but not in agricultural soils. Our results suggested that anthropogenic pressure affects higher trophic levels more than lower ones leading to a decoupled trophic structure in microbiomes. Together, our cumulative overview of microbiome patterns of bacteria and protists at the global scale revealed major patterns and differences of the trophic structure of microbiomes across Earth's habitats, and show that anthropogenic factors might have negative effects on the trophic structure within microbiomes. Furthermore, the increased impact of anthropogenic factors on especially higher trophic levels suggests that often-observed reduced ecosystem functions in anthropogenic systems might be partly attributed to a reduction of trophic complexity.


Assuntos
Ecossistema , Microbiota , Bactérias , Eucariotos , Solo , Microbiologia do Solo
8.
mBio ; 12(1)2021 02 23.
Artigo em Inglês | MEDLINE | ID: mdl-33622716

RESUMO

Microbial communities, coupled with substrate quality and availability, regulate the stock (formation versus mineralization) of soil organic matter (SOM) in terrestrial ecosystems. However, our understanding of how soil microbes interact with contrasting substrates influencing SOM quantity and quality is still very superficial. Here, we used thermodynamic theory principles and Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to evaluate the linkages between dissolved organic matter (DOM [organic substrates in soil that are readily available]), thermodynamic quality, and microbial communities. We investigated soils from subtropical paddy ecosystems across a 1,000-km gradient and comprising contrasting levels of SOM content and nutrient availability. Our region-scale study suggested that soils with a larger abundance of readily accessible resources (i.e., lower Gibbs free energy) supported higher levels of microbial diversity and higher SOM content. We further advocated a novel phylotype-level microbial classification based on their associations with OM quantities and qualities and identified two contrasting clusters of bacterial taxa: phylotypes that are highly positively correlated with thermodynamically favorable DOM and larger SOM content versus those which are associated with less-favorable DOM and lower SOM content. Both groups are expected to play critical roles in regulating SOM contents in the soil. By identifying the associations between microbial phylotypes of different life strategies and OM qualities and quantities, our study indicates that thermodynamic theory can act as a proxy for the relationship between OM and soil microbial communities and should be considered in models of soil organic matter preservation.IMPORTANCE Microbial communities are known to be important drivers of organic matter (OM) accumulation in terrestrial ecosystems. However, despite the importance of these soil microbes and processes, the mechanisms behind these microbial-SOM associations remain poorly understood. Here, we used the principles of thermodynamic theory and novel Fourier transform ion cyclotron resonance mass spectrometry techniques to investigate the links between microbial communities and dissolved OM (DOM) thermodynamic quality in soils across a 1,000-km gradient and comprising contrasting nutrient and C contents. Our region-scale study provided evidence that soils with a larger amount of readily accessible resources (i.e., lower Gibbs free energy) supported higher levels of microbial diversity and larger SOM content. Moreover, we created a novel phylotype-level microbial classification based on the associations between microbial taxa and DOM quantities and qualities. We found two contrasting clusters of bacterial taxa based on their level of association with thermodynamically favorable DOM and SOM content. Our study advances our knowledge on the important links between microbial communities and SOM. Moreover, by identifying the associations between microbial phylotypes of different life strategies and OM qualities and quantities, our study indicates that thermodynamic theory can act as a proxy for the relationship between OM and soil microbial communities. Together, our findings support that the association between microbial species taxa and substrate thermodynamic quality constituted an important complement explanation for soil organic matter preservation.

10.
Sci Rep ; 10(1): 21500, 2020 Dec 09.
Artigo em Inglês | MEDLINE | ID: mdl-33299083

RESUMO

The factors controlling the spatial variability of soil biodiversity remain largely undetermined. We conducted a global field survey to evaluate how and why the within-site spatial variability of soil biodiversity (i.e. richness and community composition) changes across global biomes with contrasting soil ages, climates and vegetation types. We found that the spatial variability of bacteria, fungi, protists, and invertebrates is positively correlated across ecosystems. We also show that the spatial variability of soil biodiversity is mainly controlled by changes in vegetation structure driven by soil age and aridity. Areas with high plant cover, but low spatial heterogeneity, were associated with low levels of spatial variability in soil biodiversity. Further, our work advances the existence of significant, undescribed links between the spatial variability of soil biodiversity and key ecosystem functions. Taken together, our findings indicate that reductions in plant cover (e.g., via desertification, increases in aridity, or deforestation), are likely to increase the spatial variability of multiple soil organisms and that such changes are likely to negatively impact ecosystem functioning across global biomes.

11.
Ecol Lett ; 2020 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-33252183

RESUMO

The biogeochemical cycling of multiple soil elements is fundamental for life on Earth. Here, we conducted a global field survey across 16 chronosequences from contrasting biomes with soil ages ranging from centuries to millions of years. For this, we collected and analysed 435 topsoil samples (0-10 cm) from 87 locations. We showed that high levels of topsoil element coupling, defined as the average correlation among nineteen soil elements, are maintained over geological timescales globally. Cross-biome changes in plant biodiversity, soil microbial structure, weathering, soil pH and texture, and mineral-free unprotected organic matter content largely controlled multi-element coupling. Moreover, elements with heavier atomic mass were naturally more decoupled and unpredictable in space than those with lighter mass. Only the coupling of carbon, nitrogen and phosphorus, which are essential to life on Earth, deviated from this predictable pattern, suggesting that this anomaly may be an undeniable fingerprint of life in terrestrial soils.

13.
ISME J ; 2020 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-33028975

RESUMO

Cropping systems have fertilized soils for decades with undetermined consequences for the productivity and functioning of terrestrial ecosystems. One of the critical unknowns is the role of soil biodiversity in controlling crop production after decades of fertilization. This knowledge gap limits our capacity to assess how changes in soil biodiversity could alter crop production and soil health in changing environments. Here, we used multitrophic ecological networks to investigate the importance of soil biodiversity, in particular, the biodiversity of key-stone taxa in controlling soil functioning and wheat production in a 35-year field fertilization experiment. We found strong and positive associations between soil functional genes, crop production and the biodiversity of key-stone phylotypes; soils supporting a larger number of key-stone nematode, bacteria and fungi phylotypes yielded the highest wheat production. These key-stone phylotypes were also positively associated with plant growth (phototrophic bacteria, nitrogen fixers) and multiple functional genes related to nutrient cycling. The retrieved information on the genomes clustered with key-stone bacterial phylotypes indicated that the key-stone taxa had higher gene copies of oxidoreductases (participating most biogeochemical cycles of ecosystems and linking to microbial energetics) and 71 essential functional genes associated with carbon, nitrogen, phosphorus, and sulfur cycling. Altogether, our work highlights the fundamental role of the biodiversity of key-stone phylotypes in maintaining soil functioning and crop production after several decades of fertilization, and provides a list of key-stone phylotypes linking to crop production and soil nutrient cycling, which could give science-based guidance for sustainable food production.

14.
Nat Commun ; 11(1): 4721, 2020 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-32948775

RESUMO

The importance of soil age as an ecosystem driver across biomes remains largely unresolved. By combining a cross-biome global field survey, including data for 32 soil, plant, and microbial properties in 16 soil chronosequences, with a global meta-analysis, we show that soil age is a significant ecosystem driver, but only accounts for a relatively small proportion of the cross-biome variation in multiple ecosystem properties. Parent material, climate, vegetation and topography predict, collectively, 24 times more variation in ecosystem properties than soil age alone. Soil age is an important local-scale ecosystem driver; however, environmental context, rather than soil age, determines the rates and trajectories of ecosystem development in structure and function across biomes. Our work provides insights into the natural history of terrestrial ecosystems. We propose that, regardless of soil age, changes in the environmental context, such as those associated with global climatic and land-use changes, will have important long-term impacts on the structure and function of terrestrial ecosystems across biomes.


Assuntos
Biota , Ecossistema , Solo/química , Bactérias/classificação , Biodiversidade , Biomassa , Clima , Fungos/classificação , Microbiota , Plantas/classificação , Fatores de Tempo
15.
Nat Commun ; 11(1): 3870, 2020 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-32747621

RESUMO

Soils harbor a substantial fraction of the world's biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.


Assuntos
Biodiversidade , Ecossistema , Microbiologia do Solo , Solo/parasitologia , Animais , Bactérias/classificação , Bactérias/metabolismo , Biomassa , Clima , Fungos/classificação , Fungos/metabolismo , Geografia , Concentração de Íons de Hidrogênio , Nematoides/classificação , Nematoides/metabolismo , Oligoquetos/classificação , Oligoquetos/metabolismo , Solo/química , Temperatura
16.
Front Plant Sci ; 11: 993, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32714361

RESUMO

The microbial communities associated with plants (the plant microbiome) play critical roles in regulating plant health and productivity. Because of this, in recent years, there have been significant increase in studies targeting the plant microbiome. Amplicon sequencing is widely used to investigate the plant microbiome and to develop sustainable microbial agricultural tools. However, performing large microbiome surveys at the regional and global scales pose several logistic challenges. One of these challenges is related with the preservation of plant materials for sequencing aiming to maintain the integrity of the original diversity and community composition of the plant microbiome. Another significant challenge involves the existence of multiple primer sets used in amplicon sequencing that, especially for bacterial communities, hampers the comparability of datasets across studies. Here, we aimed to examine the effect of different preservation approaches (snap freezing, fresh and kept on ice, and air drying) on the bacterial and fungal diversity and community composition on plant leaves, stems and roots from seven plant species from contrasting functional groups (e.g. C3, C4, N-Fixers, etc.). Another major challenge comes when comparing plant to soil microbiomes, as different primers sets are often used for plant vs. soil microbiomes. Thus, we also investigated if widely used 16S rRNA primer set (779F/1193R) for plant microbiome studies provides comparable data to those often used for soil microbiomes (341F/805R) using 86 soil samples. We found that the community composition and diversity of bacteria or fungi were robust to contrasting preservation methods. The primer sets often used for plants provided similar results to those often used for soil studies suggesting that simultaneous studies on plant and soil microbiomes are possible. Our findings provide novel evidence that preservation approaches do not significantly impact plant microbiome data interpretation and primer differences do not impact the treatment effect, which has significant implication for future large-scale and global surveys of plant microbiomes.

17.
Sci Rep ; 10(1): 11461, 2020 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-32632197

RESUMO

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

18.
Sci Rep ; 10(1): 9864, 2020 06 17.
Artigo em Inglês | MEDLINE | ID: mdl-32555419

RESUMO

This study investigated the potential role of a nitrogen-fixing early-coloniser Alnus Nepalensis D. Don (alder) in driving the changes in soil bacterial communities during secondary succession. We found that bacterial diversity was positively associated with alder growth during course of ecosystem development. Alder development elicited multiple changes in bacterial community composition and ecological networks. For example, the initial dominance of actinobacteria within bacterial community transitioned to the dominance of proteobacteria with stand development. Ecological networks approximating species associations tend to stabilize with alder growth. Janthinobacterium lividum, Candidatus Xiphinematobacter and Rhodoplanes were indicator species of different growth stages of alder. While the growth stages of alder has a major independent contribution to the bacterial diversity, its influence on the community composition was explained conjointly by the changes in soil properties with alder. Alder growth increased trace mineral element concentrations in the soil and explained 63% of variance in the Shannon-diversity. We also found positive association of alder with late-successional Quercus leucotrichophora (Oak). Together, the changes in soil bacterial community shaped by early-coloniser alder and its positive association with late-successional oak suggests a crucial role played by alder in ecosystem recovery of degraded habitats.

19.
Environ Int ; 142: 105869, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32593837

RESUMO

Microbial taxa within complex ecological networks can be classified by their universal roles based on their level of connectivity with other taxa. Highly connected taxa within an ecological network (kinless hubs) are theoretically expected to support higher levels of ecosystem functions than less connected taxa (peripherals). Empirical evidence of the role of kinless hubs in regulating the functional potential of soil microbial communities, however, is largely unexplored and poorly understood in agricultural ecosystems. Here, we built a correlation network of fungal and bacterial taxa using a large-scale survey consisting of 243 soil samples across functionally and economically important agricultural ecosystems (wheat and maize); and found that the relative abundance of taxa classified as kinless hubs within the ecological network are positively and significantly correlated with the abundance of functional genes including genes for C fixation, C degradation, C methanol, N cycling, P cycling and S cycling. Structural equation modeling of multiple soil properties further indicated that kinless hubs, but not provincial, connector or peripheral taxa, had direct significant and positive relationships with the abundance of multiple functional genes. Our findings provide novel evidence that the relative abundance of soil taxa classified as kinless hubs within microbial networks are associated with high functional potential, with implications for understanding and managing (through manipulating microbial key species) agricultural ecosystems at a large spatial scale.

20.
mSystems ; 5(3)2020 May 12.
Artigo em Inglês | MEDLINE | ID: mdl-32398279

RESUMO

The relative importance of spatial and temporal variability in shaping the distribution of soil microbial communities at a large spatial scale remains poorly understood. Here, we explored the relative importance of space versus time when predicting the distribution of soil bacterial and fungal communities across North China Plain in two contrasting seasons (summer versus winter). Although we found that microbial alpha (number of phylotypes) and beta (changes in community composition) diversities differed significantly between summer and winter, space rather than season explained more of the spatiotemporal variation of soil microbial alpha and beta diversities. Environmental covariates explained some of microbial spatiotemporal variation observed, with fast-changing environmental covariates-climate variables, soil moisture, and available nutrient-likely being the main factors that drove the seasonal variation found in bacterial and fungal beta diversities. Using random forest modeling, we further identified a group of microbial exact sequence variants (ESVs) as indicators of summer and winter seasons and for which relative abundance was associated with fast-changing environmental variables (e.g., soil moisture and dissolved organic nitrogen). Together, our empirical field study's results suggest soil microbial seasonal variation could arise from the changes of fast-changing environmental variables, thus providing integral support to the large emerging body of snapshot studies related to microbial biogeography.IMPORTANCE Both space and time are key factors that regulate microbial community, but microbial temporal variation is often ignored at a large spatial scale. In this study, we compared spatial and seasonal effects on bacterial and fungal diversity variation across an 878-km transect and found direct evidence that space is far more important than season in regulating the soil microbial community. Partitioning the effect of season, space and environmental variables on microbial community, we further found that fast-changing environmental factors contributed to microbial temporal variation.

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