scholarly journals Soil disturbance affects plant growth via soil microbial community shifts

2020 ◽  
Author(s):  
Taylor J. Seitz ◽  
Ursel M. E. Schütte ◽  
Devin M. Drown
Keyword(s):  
Microbial Community ◽  
Plant Growth ◽  
Microbial Communities ◽  
Boreal Forests ◽  
Soil Disturbance ◽  
Metagenomic Sequencing ◽  
Permafrost Thaw ◽  
Undisturbed Soils ◽  
Community Shifts ◽  
Thawing Permafrost

AbstractRecent advances in climate research have discovered that permafrost is particularly vulnerable to the changes occurring in the atmosphere and climate, especially in Alaska where 85% of the land is underlain by mostly discontinuous permafrost. As permafrost thaws, research has shown that natural and anthropogenic soil disturbance causes microbial communities to undergo shifts in membership composition and biomass, as well as in functional diversity. Boreal forests are home to many plants that are integral to the subsistence diets of many Alaska Native communities. Yet, it is unclear how the observed shifts in soil microbes can affect above ground plant communities that are relied on as a major source of food. In this study, we tested the hypothesis that microbial communities associated with permafrost thaw affect plant growth by growing five plant species found in Boreal forests and Tundra ecosystems, including low-bush cranberry and bog blueberry, with microbial communities from the active layer soils of a permafrost thaw gradient. We found that plant growth was significantly affected by the microbial soil inoculants. Plants inoculated with communities from above thawing permafrost showed decreased growth compared to plants inoculated with microbes from undisturbed soils. We used metagenomic sequencing to determine that microbial communities from disturbed soils above thawing permafrost have differences in taxonomy from microbial communities in undisturbed soils above intact permafrost. The combination of these results indicates that a decrease in plant growth can be linked to soil disturbance driven changes in microbial community membership and abundance. These data contribute to an understanding of how microbial communities can be affected by soil disturbance and climate change, and how those community shifts can further influence plant growth in Boreal forests and more broadly, ecosystem health.

scholarly journals Soil Disturbance Affects Plant Productivity via Soil Microbial Community Shifts

2021 ◽  
Vol 12 ◽  
Author(s):  
Taylor J. Seitz ◽  
Ursel M. E. Schütte ◽  
Devin M. Drown
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Boreal Forests ◽  
Plant Productivity ◽  
Soil Disturbance ◽  
Metagenomic Sequencing ◽  
Permafrost Thaw ◽  
Undisturbed Soils ◽  
Community Shifts ◽  
Thawing Permafrost

Recent advances in climate research have discovered that permafrost is particularly vulnerable to the changes occurring in the atmosphere and climate, especially in Alaska where 85% of the land is underlain by mostly discontinuous permafrost. As permafrost thaws, research has shown that natural and anthropogenic soil disturbance causes microbial communities to undergo shifts in membership composition and biomass, as well as in functional diversity. Boreal forests are home to many plants that are integral to the subsistence diets of many Alaska Native communities. Yet, it is unclear how the observed shifts in soil microbes can affect above ground plant communities that are relied on as a major source of food. In this study, we tested the hypothesis that microbial communities associated with permafrost thaw affect plant productivity by growing five plant species found in Boreal forests and Tundra ecosystems, including low-bush cranberry and bog blueberry, with microbial communities from the active layer soils of a permafrost thaw gradient. We found that plant productivity was significantly affected by the microbial soil inoculants. Plants inoculated with communities from above thawing permafrost showed decreased productivity compared to plants inoculated with microbes from undisturbed soils. We used metagenomic sequencing to determine that microbial communities from disturbed soils above thawing permafrost differ in taxonomy from microbial communities in undisturbed soils above intact permafrost. The combination of these results indicates that a decrease in plant productivity can be linked to soil disturbance driven changes in microbial community membership and abundance. These data contribute to an understanding of how microbial communities can be affected by soil disturbance and climate change, and how those community shifts can further influence plant productivity in Boreal forests and more broadly, ecosystem health.

scholarly journals Patterns in the Microbial Community of Salt-Tolerant Plants and the Functional Genes Associated with Salt Stress Alleviation

2021 ◽  
Author(s):  
Yanfen Zheng ◽  
Zongchang Xu ◽  
Haodong Liu ◽  
Yan Liu ◽  
Yanan Zhou ◽  
...  
Keyword(s):  
Salt Stress ◽  
Microbial Community ◽  
Plant Growth ◽  
Microbial Communities ◽  
Functional Genes ◽  
Genomic Information ◽  
Salt Tolerant ◽  
Comprehensive Understanding ◽  
Stress Alleviation ◽  
Tolerant Plants

Salinity is an important but little-studied abiotic stressor affecting plant growth. Although several previous reports have examined salt-tolerant plant microbial communities, we still lack a comprehensive understanding about the functional characteristics and genomic information of this population.

scholarly journals Succession of bacterial communities on carrion is independent of vertebrate scavengers

2019 ◽  
Author(s):  
Cody R. Dangerfield ◽  
Ethan Frehner ◽  
Evan Buechley ◽  
Çağan H. Şekercioğlu ◽  
William J. Brazelton
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Rrna Gene ◽  
Scavenging Activity ◽  
Ecological Interactions ◽  
Tissue Samples ◽  
Ultimate Result ◽  
Community Shifts ◽  
Micro Organisms ◽  
Carrion Decomposition

AbstractThe decomposition of carrion is carried out by a suite of macro- and micro-organisms who interact with each other in a variety of ecological contexts. The ultimate result of carrion decomposition is the recycling of carbon and nutrients from the carrion back into the ecosystem. Exploring these ecological interactions among animals and microbes is a critical aspect of understanding the nutrient cycling of an ecosystem. Here we investigate the potential impacts that vertebrate scavenging may have on the microbial community of carrion. In this study, we placed seven juvenile domestic cow carcasses in the Grassy Mountain region of Utah, USA and collected tissue samples at periodic intervals. Using high-depth environmental sequencing of the 16S rRNA gene and camera trap data, we documented the microbial community shifts associated with decomposition and with vertebrate scavenger visitation. The remarkable scarcity of animals at our study site enabled us to examine natural carrion decomposition in the near absence of animal scavengers. Our results indicate that the microbial communities of carcasses that experienced large amounts of scavenging activity were not significantly different than those carcasses that observed very little scavenging activity. Rather, the microbial community shifts reflected changes in the stage of decomposition similar to other studies documenting the successional changes of carrion microbial communities. Our study suggests that microbial community succession on carrion follows consistent patterns that are largely unaffected by scavenging.

Relationships between Arabidopsis genotype-specific biomass accumulation and associated soil microbial communities

Botany ◽  
2013 ◽  
Vol 91 (2) ◽  
pp. 123-126 ◽  
Author(s):  
Akifumi Sugiyama ◽  
Matthew G. Bakker ◽  
Dayakar V. Badri ◽  
Daniel K. Manter ◽  
Jorge M. Vivanco
Keyword(s):  
Microbial Community ◽  
Plant Growth ◽  
Growth Performance ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
454 Sequencing ◽  
Biomass Accumulation ◽  
The United States ◽  
Natural Soil ◽  
Soil Microbial

Rhizosphere microbial communities are impacted by resident plant species and have reciprocal effects on their host plants. We collected resident soil from five wild populations of Arabidopsis in the United States and Europe in an effort to characterize the impacts of natural soil microbiomes on Arabidopsis growth performance. The microbial communities present in these soils showed differences in community structure as assessed by 454 sequencing and in metabolic activity. While pathogens associated with the Brassica family were rare, diverse genera of potential plant growth promoting rhizobacteria were detected. Seed corresponding to the five Arabidopsis genotypes was grown in resident and nonresident soils to determine relationships among plant growth performance and soil microbial community and edaphic characteristics. Arabidopsis genotypes demonstrated different patterns of relationship between biomass accumulation and microbial community characteristics. This work sheds light on the bacterial populations naturally associated with Arabidopsis and suggests implications of the rhizosphere microbiome for plant growth performance.

scholarly journals Plant species and soil type influence rhizosphere bacterial composition and seedling establishment on serpentine soils

2018 ◽  
Author(s):  
Alexandria N. Igwe ◽  
Rachel L. Vannette
Keyword(s):  
Microbial Community ◽  
Plant Growth ◽  
Microbial Communities ◽  
Plant Species ◽  
Soil Chemistry ◽  
Seedling Survival ◽  
Serpentine Soils ◽  
Bacterial Composition ◽  
Plant Phenotype ◽  
Community Source

AbstractRoot-associated microbial communities influence plant phenotype, growth and local abundance, yet the factors that structure these microbial communities are still poorly understood. California landscapes contain serpentine soils, which are nutrient-poor and high in heavy metals, and distinct from neighboring soils. Here, we surveyed the rhizoplane of serpentine-indifferent plants species growing on serpentine and non-serpentine soils to determine the relative influence of plant identity and soil chemistry on rhizoplane microbial community structure using 16S rRNA metabarcoding. Additionally, we experimentally examined if locally adapted microorganisms enhance plant growth in serpentine soil. Plant species, soil chemistry, and the interaction between them were important in structuring rhizoplane bacterial communities in both the field and experimental soils. In the experiment, rhizoplane microbial community source influenced seedling survival, but plant growth phenotypes measured were largely invariant to microbial community with a few exceptions. Results from the field sampling suggest that plant species associate with specific microbial communities even across chemically distinct soils, and that microbial communities can differentially influence seedling survival on harsh serpentine soils.

scholarly journals The structure and function of the rhizosphere microbial communities of Carex praeclara and Leymus secalinus in a Zoige alpine grassland

2021 ◽  
Author(s):  
TingKun Jian ◽  
Yue Xia ◽  
Ruipeng He ◽  
Jie zhang
Keyword(s):  
Plant Growth ◽  
Microbial Communities ◽  
Stress Responses ◽  
Rhizosphere Soil ◽  
Growth Promotion ◽  
Structure And Function ◽  
Vegetation Coverage ◽  
Metagenomic Sequencing ◽  
Alpine Sandy Land ◽  
And Function

Rhizosphere microorganisms are thought to play a crucial role in the promotion of plant growth and health. Carex praeclara and Leymus secalinus are dominant plant species that have colonized the desertification land of Alpine wetland grasslands in Zoige. There is a lack of comprehensive research on their rhizosphere microbes. In this study, we used deep shotgun metagenomic sequencing to analyze the microbial community and functional composition of the rhizosphere and corresponding non-rhizosphere soils of C. praeclara and L. secalinus. The microbial diversity and structure exhibited a remarkable difference among the rhizosphere and non-rhizosphere samples, and the predominant taxa included Actinobacteria, Proteobacteria, Acidobacteria and Chloroflexi in all the samples. Genes that were over-represented include those involved in the acquisition of nutrients, stress responses, transposable elements and plant growth promotion suggest that the interactions between microbe-plant and microbe-microbe are more intense in the rhizosphere soil. The relative abundances of pivotal genes that participate in microbial nitrogen (N) and phosphorus (P) transformation were higher in the rhizosphere soil than in the non-rhizosphere soil, indicating the enhancement of potential soil N- and P-cycling in the plant rhizosphere. Our findings provide valuable information on the structure and function of the microbial communities of the C. praeclara and L. secalinus rhizospheres and lay a foundation for the further use of C. praeclara and L. secalinus to increase vegetation coverage, improve soil properties and restore the ecological function of degraded alpine sandy land.

scholarly journals Geochemical and metagenomic characterization of Jinata Onsen, a Proterozoic-analog hot spring, reveals novel microbial diversity including iron-tolerant phototrophs and thermophilic lithotrophs

2018 ◽  
Author(s):  
Lewis M. Ward ◽  
Airi Idei ◽  
Mayuko Nakagawa ◽  
Yuichiro Ueno ◽  
Woodward W. Fischer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Ferrous Iron ◽  
Hot Springs ◽  
Hot Spring ◽  
Spatial Scales ◽  
Oxygenic Photosynthesis ◽  
Metagenomic Sequencing ◽  
Geochemical Conditions

AbstractHydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interaction between the reducing hydrothermal fluids, the oxygenated atmosphere, and in some cases seawater. At Jinata Onsen, on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating a diversity of chemical potentials and redox pairs over a distance ~10 m. We characterized the geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse via 16S rDNA amplicon and genome-resolved shotgun metagenomic sequencing. The microbial community changed significantly downstream as temperatures and dissolved iron concentrations decreased and dissolved oxygen increased. Near the spring source, biomass is limited relative to downstream, and primary productivity may be fueled by oxidation of ferrous iron and molecular hydrogen by members of the Zetaproteobacteria and Aquificae. Downstream, the microbial community is dominated by oxygenic Cyanobacteria. Cyanobacteria are abundant and active even at ferrous iron concentrations of ~150 μM, which challenges the idea that iron toxicity limited cyanobacterial expansion in Precambrian oceans. Several novel lineages of Bacteria are also present at Jinata Onsen, including previously uncharacterized members of the Chloroflexi and Caldithrichaeota phyla, positioning Jinata Onsen as a valuable site for future characterization of these clades.ImportanceHigh temperatures and reducing conditions allow hot springs to support microbial communities that are very different from those found elsewhere on the surface of the Earth today; in some ways, these environments and the communities they support can be similar to environments that existed on the early Earth and that may exist on other planets. Here, we describe a novel hot spring system where hot, iron-rich but oxygen-poor water flows into the ocean, supporting a range of unique microbial communities. Metagenomic sequencing recovered many novel microbial lineages, including deep-branching and uniquely thermotolerant members of known groups. Comparison of the biological communities in the upstream part of the hot spring, potentially supported by biological iron and hydrogen oxidizing metabolisms, to downstream microbial mats, supported by oxygenic photosynthesis, provides insight into the potential productivity of life during Proterozoic time and on other planets where oxygenic photosynthesis is not possible.

scholarly journals Unearthing Shifts in Microbial Communities Across a Soil Disturbance Gradient

2021 ◽  
Author(s):  
Taylor J Seitz ◽  
Ursel M.E. Schütte ◽  
Devin M Drown
Keyword(s):  
Climate Change ◽  
Plant Growth ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Soil Disturbance ◽  
The Arctic ◽  
Metagenomic Data ◽  
Undisturbed Soil ◽  
Disturbed Soil ◽  
Disturbance Gradient

Permafrost, an important source of soil disturbance, is particularly vulnerable to climate change in Alaska where 85% of the land is underlain with discontinuous permafrost. Boreal forests, home to plants integral to subsistence diets of many Alaska Native communities, are not immune to the effects of climate change. Soil disturbance events such as permafrost thaw, wildfires, and land use change can influence abiotic conditions which can then affect active layer soil microbial communities. Previously, we found negative effects on boreal plants inoculated with microbes impacted by soil disturbance compared to plants inoculated with microbes from undisturbed soils. Here, we identify the key shifts in microbial inoculant communities altered by soil disturbance using 16S rRNA amplicon sequencing as well as changes in potential functional mechanisms that influence plant growth using long read metagenomics. Across our soil disturbance gradient, microbial communities differ significantly based on the level of soil disturbance. Consistent with previous results, the family Acidobacteriaceae, which consists of known plant promoters, was abundant in undisturbed soil, but practically absent in most disturbed soil. In contrast, Comamonadaceae, a family with known agricultural pathogens, was overrepresented in most disturbed soil communities compared to undisturbed. Within our metagenomic data, we found that soil disturbance level drives differences in microbial community function. These results indicate that a decrease in plant growth can be linked to changes in the community and functional composition driven by soil disturbance and climate change. Together these results build a genomic understanding of how shifting soil microbiomes may affect plant productivity and ecosystem health as the Arctic warms.

scholarly journals Small subsets of highly connected taxa predict compositional change in microbial communities

2017 ◽  
Author(s):  
Cristina M. Herren ◽  
Katherine D. McMahon
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Dynamics ◽  
External Disturbance ◽  
Biotic Interactions ◽  
Microbial Community Dynamics ◽  
Community Turnover ◽  
Community Shifts ◽  
Curtis Dissimilarity ◽  
Community Connectivity

AbstractFor decades, ecological theory has predicted that the complexity of communities should be related to their stability. However, this prediction has rarely been tested empirically, because of both the difficulty of finding suitable systems where the question is tractable and the trouble of defining “stability” in real systems. Microbial communities provide the opportunity to investigate a related question: how does community connectivity relate to the rate of compositional turnover? We used a newly developed metric called community “cohesion” to test how microbial community connectivity relates to Bray-Curtis dissimilarity through time. In three long-term datasets, we found that stronger connectivity corresponded to lower rates of compositional turnover. Using two case studies of disturbed and reference communities, we found that the predictive power of community connectivity was diminished by external disturbance. Finally, we tested whether the highly connected taxa were disproportionately important in explaining compositional turnover. We found that subsets of highly connected “keystone” taxa, generally comprising 1-5% of community richness, explained community turnover better than using all taxa. Our results suggest that stronger biotic interactions within microbial community dynamics are stabilizing to community composition, and that highly connected taxa are good indicators of pending community shifts.

scholarly journals Predominance of Anaerobic, Spore-Forming Bacteria in Metabolically Active Microbial Communities from Ancient Siberian Permafrost

2019 ◽  
Vol 85 (15) ◽  
Author(s):  
Renxing Liang ◽  
Maggie Lau ◽  
Tatiana Vishnivetskaya ◽  
Karen G. Lloyd ◽  
Wei Wang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Aspartic Acid ◽  
Early Pleistocene ◽  
Metagenomic Sequencing ◽  
Metabolic Functions ◽  
Northeastern Siberia ◽  
Spore Forming Bacteria

ABSTRACTThe prevalence of microbial life in permafrost up to several million years (Ma) old has been well documented. However, the long-term survivability, evolution, and metabolic activity of the entombed microbes over this time span remain underexplored. We integrated aspartic acid (Asp) racemization assays with metagenomic sequencing to characterize the microbial activity, phylogenetic diversity, and metabolic functions of indigenous microbial communities across a ∼0.01- to 1.1-Ma chronosequence of continuously frozen permafrost from northeastern Siberia. Although Asp in the older bulk sediments (0.8 to 1.1 Ma) underwent severe racemization relative to that in the youngest sediment (∼0.01 Ma), the much lowerd-Asp/l-Asp ratio (0.05 to 0.14) in the separated cells from all samples suggested that indigenous microbial communities were viable and metabolically active in ancient permafrost up to 1.1 Ma. The microbial community in the youngest sediment was the most diverse and was dominated by the phylaActinobacteriaandProteobacteria. In contrast, microbial diversity decreased dramatically in the older sediments, and anaerobic, spore-forming bacteria withinFirmicutesbecame overwhelmingly dominant. In addition to the enrichment of sporulation-related genes, functional genes involved in anaerobic metabolic pathways such as fermentation, sulfate reduction, and methanogenesis were more abundant in the older sediments. Taken together, the predominance of spore-forming bacteria and associated anaerobic metabolism in the older sediments suggest that a subset of the original indigenous microbial community entrapped in the permafrost survived burial over geological time.IMPORTANCEUnderstanding the long-term survivability and associated metabolic traits of microorganisms in ancient permafrost frozen millions of years ago provides a unique window into the burial and preservation processes experienced in general by subsurface microorganisms in sedimentary deposits because of permafrost’s hydrological isolation and exceptional DNA preservation. We employed aspartic acid racemization modeling and metagenomics to determine which microbial communities were metabolically active in the 1.1-Ma permafrost from northeastern Siberia. The simultaneous sequencing of extracellular and intracellular genomic DNA provided insight into the metabolic potential distinguishing extinct from extant microorganisms under frozen conditions over this time interval. This in-depth metagenomic sequencing advances our understanding of the microbial diversity and metabolic functions of extant microbiomes from early Pleistocene permafrost. Therefore, these findings extend our knowledge of the survivability of microbes in permafrost from 33,000 years to 1.1 Ma.

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