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 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 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.

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 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.

A chronsequential approach to investigating microbial community shifts following clearcutting in Boreal Plain forest soils

2012 ◽  
Vol 42 (12) ◽  
pp. 2078-2089 ◽  
Author(s):  
Holly M. Hynes ◽  
James J. Germida
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
16S Rdna ◽  
Community Composition ◽  
Soil Microbial Communities ◽  
Forest Harvesting ◽  
Soil Parameters ◽  
Community Size ◽  
Post Harvest ◽  
Community Shifts

Impacts of forest harvesting are often assessed in short-term studies that ignore the longer term changes associated with the disturbance. A chronosequence approach was taken to investigate changes in microbial community size and composition over ∼20 years post-harvest in lodgepole pine ( Pinus contorta Douglas ex Loudon) stands of the Boreal Plain. The LFH and mineral Ae horizons of Orthic Gray Luvisolic soils were sampled in six cutblocks, aged 1–19 years since harvest, in 2009 and 2010. Changes in microbial communities were assessed using phospholipid fatty acid analysis (PLFA) and 16S rDNA analysis. Physical and chemical soil parameters were measured to delineate microsite changes impacting microbial community shifts. Total microbial biomass (PLFA) was unaffected by harvesting disturbance, although fungal biomass was significantly larger in the oldest cutblock of the chronosequence. Microbial community composition did, however, differ between younger and older cutblocks as indicated by both lipid PLFA and 16S rDNA fingerprinting techniques. Forest soil microbial communities subject to clearcutting were observed to shift in overall community composition while remaining consistent in overall community size. The shift in community composition, which occurred in concert with the maintenance of biomass, indicated that the microbial community adapted sufficiently to the new post-harvest microsite conditions.

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

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9307 ◽  
Author(s):  
Cody R. Dangerfield ◽  
Ethan H. Frehner ◽  
Evan R. 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

The 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 vertebrate scavenging.

scholarly journals Slope Aspect Affects The Soil Microbial Communities In Karst Tiankeng Negative Landforms

2021 ◽  
Author(s):  
Cong Jiang ◽  
Wei Shui ◽  
Su-Feng Zhu ◽  
Jie Feng
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Large Scale ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Slope Aspect ◽  
Soil Conditions ◽  
Metagenomic Sequencing ◽  
Soil Microbial

Abstract Background: Karst tiankeng is a large-scale negative surface terrain, and slope aspect affect the soil conditions, vegetation and microbial flora in the tiankeng. However, the influence of the slope aspect on the soil microbial community in tiankeng has not been elucidated. Methods: In this study, metagenomic sequencing technology was used to analyzed the soil microbial communities and metabolic function on the shady and sunny slopes of karst tiankeng. Results: The Shannon-Wiener diversity of microbial communities on shady slopes was significantly higher than that on shady slopes. Shady and sunny slopes have similar microbial community composition, but there are differences in abundance. The linear discriminate analysis (LDA) results showed that biomarkers mainly belongs to Actinobacteria, Chloroflexi and Proteobacteria. Functional pathways and CAZy (Carbohydrate-Active Enzymes) genes also had a remarkable response to slope aspect change. LEfSe results indicated several biomarker pathways in sunny slope involved in human disease. Moreover, the abundance of CAZy genes was higher in shady slope and had stronger ability in decomposing litter. The microbial communities were mainly correlation with the vegetation characteristics (species richness and coverage) and soil properties (SOM and pH). Conclusions: These results indicate slope aspect has a pronounced influence on microbial community composition, structure and function at karst tiankeng. In the future, the conservation of karst tiankeng biodiversity should pay more attention to topographical factors.

A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Environmental Remediation ◽  
Real Life ◽  
Design Principles ◽  
Microbial Interactions ◽  
Potential Applications ◽  
New Gene ◽  
Global Biogeochemical Cycles ◽  
Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

scholarly journals CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

2021 ◽  
Vol 9 (4) ◽  
pp. 816
Author(s):  
Matthew G. Links ◽  
Tim J. Dumonceaux ◽  
E. Luke McCarthy ◽  
Sean M. Hemmingsen ◽  
Edward Topp ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Shotgun Sequencing ◽  
Natural Ecosystems ◽  
Gene Markers ◽  
Microbial Profile ◽  
Microbial Ecosystems ◽  
Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

Sign in / Sign up

Export Citation Format

Share Document