scholarly journals Spatial gradients in soil-carbon character of a coastal forested floodplain are associated with abiotic features, but not microbial communities

2019 ◽  
Author(s):  
Aditi Sengupta ◽  
Julia Indivero ◽  
Cailene Gunn ◽  
Malak M. Tfaily ◽  
Rosalie K. Chu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Organic Compounds ◽  
Community Composition ◽  
Community Assembly ◽  
Dispersal Limitation ◽  
Water Soluble ◽  
Microbial Composition ◽  
Organic C ◽  
Shallow Soils

Abstract. Coastal terrestrial-aquatic interfaces (TAIs) are dynamic zones of biogeochemical cycling influenced by salinity gradients. However, there is significant heterogeneity in salinity influences on TAI soil biogeochemical function. This heterogeneity is perhaps related to unrecognized mechanisms associated with carbon (C) chemistry and microbial communities. To investigate this potential, we evaluated hypotheses associated with salinity-associated shifts in organic C thermodynamics, biochemical transformations, and heteroatom content in a first-order coastal watershed in the Olympic Peninsula of Washington state, USA. In contrast to our hypotheses, thermodynamic favorability of water soluble organic compounds in shallow soils decreased with increasing salinity, as did the number of inferred biochemical transformations and total heteroatom content. These patterns indicate lower microbial activity at higher salinity that is potentially constrained by accumulation of less favorable organic C. Furthermore, organic compounds appeared to be primarily marine/algal-derived in forested floodplain soils with more lipid-like and protein-like compounds, relative to upland soils that had more lignin-, tannin-, and carbohydrate-like compounds. Based on a recent simulation-based study, we further hypothesized a relationship between microbial community assembly processes and C chemistry. Null modelling revealed strong influences of dispersal limitation over microbial composition, which may be due to limited hydrologic connectivity within the clay-rich soils. Dispersal limitation indicated stochastically assembled communities, which was further reflected in the lack of an association between community assembly processes and C chemistry. This suggests a disconnect between microbial community composition and C biogeochemistry, thereby indicating that the salinity-associated gradient in C chemistry was driven by a combination of spatially-structured inputs and salinity-associated metabolic responses of microbial communities that were independent of community composition. We propose that impacts of salinity on coastal soil biogeochemistry need to be understood in the context of C chemistry, hydrologic/depositional dynamics, and microbial physiology, while microbial composition may have less influence.

scholarly journals Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities

2019 ◽  
Vol 16 (19) ◽  
pp. 3911-3928 ◽  
Author(s):  
Aditi Sengupta ◽  
Julia Indivero ◽  
Cailene Gunn ◽  
Malak M. Tfaily ◽  
Rosalie K. Chu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Organic Compounds ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Water Soluble ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Organic C ◽  
Shallow Soils

Abstract. Coastal terrestrial–aquatic interfaces (TAIs) are dynamic zones of biogeochemical cycling influenced by salinity gradients. However, there is significant heterogeneity in salinity influences on TAI soil biogeochemical function. This heterogeneity is perhaps related to unrecognized mechanisms associated with carbon (C) chemistry and microbial communities. To investigate this potential, we evaluated hypotheses associated with salinity-associated shifts in organic C thermodynamics; biochemical transformations; and nitrogen-, phosphorus-, and sulfur-containing heteroatom organic compounds in a first-order coastal watershed on the Olympic Peninsula of Washington, USA. In contrast to our hypotheses, thermodynamic favorability of water-soluble organic compounds in shallow soils decreased with increasing salinity (43–867 µS cm−1), as did the number of inferred biochemical transformations and total heteroatom content. These patterns indicate lower microbial activity at higher salinity that is potentially constrained by accumulation of less-favorable organic C. Furthermore, organic compounds appeared to be primarily marine- or algae-derived in forested floodplain soils with more lipid-like and protein-like compounds, relative to upland soils that had more lignin-, tannin-, and carbohydrate-like compounds. Based on a recent simulation-based study, we further hypothesized a relationship between C chemistry and the ecological assembly processes governing microbial community composition. Null modeling revealed that differences in microbial community composition – assayed using 16S rRNA gene sequencing – were primarily the result of limited exchange of organisms among communities (i.e., dispersal limitation). This results in unstructured demographic events that cause community composition to diverge stochastically, as opposed to divergence in community composition being due to deterministic selection-based processes associated with differences in environmental conditions. The strong influence of stochastic processes was further reflected in there being no statistical relationship between community assembly processes (e.g., the relative influence of stochastic assembly processes) and C chemistry (e.g., heteroatom content). This suggests that microbial community composition does not have a mechanistic or causal linkage to C chemistry. The salinity-associated gradient in C chemistry was, therefore, likely influenced by a combination of spatially structured inputs and salinity-associated metabolic responses of microbial communities that were independent of community composition. We propose that impacts of salinity on coastal soil biogeochemistry need to be understood in the context of C chemistry, hydrologic or depositional dynamics, and microbial physiology, while microbial composition may have less influence.

scholarly journals Response of Microbial Communities on Culturing Plates of Post-settlement Sea Cucumbers to Seawater Acidification and Warming

2021 ◽  
Vol 8 ◽  
Author(s):  
Hongxia Zhang ◽  
Mingshan Song ◽  
Lili Wang ◽  
Anguo Zhang ◽  
Xiaolong Yang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Apostichopus Japonicus ◽  
Bacterial Community Composition ◽  
Early Period ◽  
Control Group ◽  
Microbial Composition ◽  
Seawater Acidification ◽  
Corrugated Plates

Seawater acidification and warming have been found to affect the early life of many marine organisms, but their effects on the microbial community in the environment related to the early development stage of aquaculture species have been rarely investigated. To understand how seawater acidification and warming impact the microbial community in aquaculture systems, we designed four microcosms to monitor and characterize the microbial composition on the corrugated plates in the Apostichopus japonicus culture tanks during its post-settlement stage. High-throughput 16S rRNA sequencing revealed that the bacterial community composition varied significantly in different periods of incubation. The bacterial diversity and community composition were obviously changed by seawater acidification and warming in the early period and then tended to revert to the level of the control group. Acidification significantly increased the relative abundance of dominant families Rhodobacteraceae and Flavobacteriaceae in the early period, suggesting that microbiota could increase the abundance of predominant taxa to adapt to increased CO2 concentration and reconstruct a stable community structure. No interaction effect of both factors was observed in the combined group. Results reveal that the microbial communities on the corrugated plates in A. japonicus culture tank were affected in the early period of incubation, and could then acclimatize to the increased CO2 and temperature. This study provides new insights into the variation and adaptation responses of the microbiota in aquaculture systems to seawater acidification and warming.

scholarly journals Spatial Diversity in Bacterial Communities across Barren and Vegetated, Native and Invasive, Coastal Dune Microhabitats

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 525
Author(s):  
Brianna L. Boss ◽  
Bianca R. Charbonneau ◽  
Javier A. Izquierdo
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Plant Species ◽  
Bacterial Communities ◽  
Environmental Gradients ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Spatial Diversity ◽  
Microbial Composition

The microbial community composition of coastal dunes can vary across environmental gradients, with the potential to impact erosion and deposition processes. In coastal foredunes, invasive plant species establishment can create and alter environmental gradients, thereby altering microbial communities and other ecogeomorphic processes with implications for storm response and management and conservation efforts. However, the mechanisms of these processes are poorly understood. To understand how changing microbial communities can alter these ecogeomorphic dynamics, one must first understand how soil microbial communities vary as a result of invasion. Towards this goal, bacterial communities were assessed spatially along foredune microhabitats, specifically in barren foredune toe and blowout microhabitats and in surrounding vegetated monocultures of native Ammophila breviligulata and invasive Carex kobomugi. Across dune microhabitats, microbial composition was more dissimilar in barren dune toe and blowout microhabitats than among the two plant species, but it did not appear that it would favor the establishment of one plant species over the other. However, the subtle differences between the microbial community composition of two species could ultimately aid in the success of the invasive species by reducing the proportions of bacterial genera associated exclusively with A. breviligulata. These results suggest that arrival time may be crucial in fostering microbiomes that would further the continued establishment and spread of either plant species.

scholarly journals Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities

2018 ◽  
Author(s):  
Eric M. Bottos ◽  
David W. Kennedy ◽  
Elvira B. Romero ◽  
Sarah J. Fansler ◽  
Joseph M. Brown ◽  
...  
Keyword(s):  
Microbial Community ◽  
Variable Selection ◽  
Microbial Communities ◽  
Community Composition ◽  
Structural Equation ◽  
Microbial Community Composition ◽  
Dispersal Limitation ◽  
Equation Modeling ◽  
Permafrost Soil ◽  
Total Selection

AbstractUnderstanding drivers of permafrost microbial community composition is critical for understanding permafrost microbiology and predicting ecosystem responses to thaw, however studies describing ecological controls on these communities are lacking. We hypothesize that permafrost communities are uniquely shaped by constraints imposed by prolonged freezing, and decoupled from factors that influence non-permafrost soil communities. To test this hypothesis, we characterized patterns of environmental variation and microbial community composition in permafrost across an Alaskan boreal forest landscape. We used null modeling to estimate the relative importance of selective and neutral assembly processes on community composition, and identified environmental factors influencing ecological selection through regression and structural equation modeling (SEM). Proportionally, the strongest process influencing community composition was dispersal limitation (0.36), exceeding the influence of homogenous selection (0.21), variable selection (0.16), and homogenizing dispersal (0.05). Fe(II) content was the most important factor explaining variable selection, and was significantly associated with total selection by univariate regression (R2=0.14, p=0.003). SEM supported a model in which Fe(II) content mediated influences of the Gibbs free energy of the organic matter pool and organic acid concentration on total selection. These findings reveal that the processes shaping microbial communities in permafrost are distinct from those in non-permafrost soils, as the stability of the permafrost environment imposes dispersal and thermodynamic constraints on permafrost communities. Models of permafrost community composition will need to account for these unique drivers in order to predict community characteristics across permafrost landscapes, and in efforts to understand how pre-thaw conditions will influence post-thaw ecological and biogeochemical processes.

scholarly journals Disturbance and recovery: a synthesis of microbial community reassembly following disturbance across realms

2021 ◽  
Author(s):  
Stephanie Jurburg ◽  
Shane Blowes ◽  
Ashley Shade ◽  
Nico Eisenhauer ◽  
Jonathan Chase
Keyword(s):  
Time Series ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Community Assembly ◽  
Disturbance And Recovery ◽  
Microbial Community Assembly ◽  
Community Reassembly ◽  
Over Time

Disturbances alter the diversity and composition of microbial communities, but whether microbiomes from different environments exhibit similar degrees of resistance or rates of recovery has not been evaluated. Here, we synthesized 86 time series of disturbed mammalian, aquatic, and soil microbiomes to examine how the recovery of microbial richness and community composition differed after disturbance. We found no general patterns in compositional variance (i.e., dispersion) in any microbiomes over time. Only mammalian microbiomes consistently exhibited decreases in richness following disturbance. Importantly, they tended to recover this richness, but not their composition, over time. In contrast, aquatic microbiomes tended to diverge from their pre-disturbance composition following disturbance. By synthesizing microbiome responses across environments, our study aids in the reconciliation of disparate microbial community assembly frameworks, and highlights the role of the environment in microbial community reassembly following disturbance.

scholarly journals Nutritional Composition and Microbial Communities of Two Non-alcoholic Traditional Fermented Beverages from Zambia: A Study of Mabisi and Munkoyo

Nutrients ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1628 ◽  
Author(s):  
Justin Chileshe ◽  
Joost van den Heuvel ◽  
Ray Handema ◽  
Bas J Zwaan ◽  
Elise F. Talsma ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Raw Materials ◽  
Microbial Community Composition ◽  
Nutritional Composition ◽  
Fermented Foods ◽  
Microbial Composition ◽  
Specific Product ◽  
Traditional Fermented Foods

Traditional fermented foods and beverages are common in many countries, including Zambia. While the general (nutritional) benefits of fermented foods are widely recognised, the nutritional composition of most traditional fermented foods is unknown. Furthermore, fermentation is known to add nutritional value to raw materials, mainly by adding B-vitamins and removing anti-nutritional factors. In the case of traditional fermentation, the composition of microbial communities responsible for fermentation varies from producer to producer and this may also be true for the nutritional composition. Here, we characterized the nutrient profile and microbial community composition of two traditional fermented foods: milk-based Mabisi and cereal-based Munkoyo. We found that the two products are different with respect to their nutritional parameters and their microbial compositions. Mabisi was found to have higher nutritional values for crude protein, fat, and carbohydrates than Munkoyo. The microbial community composition was also different for the two products, while both communities were dominated by lactic acid bacteria. Our analyses showed that variations in nutritional composition, defined as the amount of consumption that would contribute to the estimated average requirement (EAR), might be explained by variations in microbial community composition. Consumption of Mabisi appeared to contribute more than Munkoyo to the EAR and its inclusion in food-based recommendations is warranted. Our results show the potential of traditional fermented foods such as Mabisi and Munkoyo to add value to current diets and suggests that variations in microbial composition between specific product samples can result in variations in nutritional composition.

scholarly journals Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 865
Author(s):  
Lantian Su ◽  
Xinxin Liu ◽  
Guangyao Jin ◽  
Yue Ma ◽  
Haoxin Tan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Environmental Factors ◽  
Microbial Communities ◽  
Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Functional Genes ◽  
Martes Zibellina ◽  
Clear Cutting ◽  
Metabolic Functions

In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.

scholarly journals Assembly processes of gastropod community change with horizontal and vertical zonation in ancient Lake Ohrid: a metacommunity speciation perspective

2016 ◽  
Vol 13 (10) ◽  
pp. 2901-2911 ◽  
Author(s):  
Torsten Hauffe ◽  
Christian Albrecht ◽  
Thomas Wilke
Keyword(s):  
Community Composition ◽  
Community Assembly ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Species Interaction ◽  
Relative Importance ◽  
Lake Depth ◽  
Ancient Lake ◽  
Lake Ohrid ◽  
Speciation Model

Abstract. The Balkan Lake Ohrid is the oldest and most diverse freshwater lacustrine system in Europe. However, it remains unclear whether species community composition, as well as the diversification of its endemic taxa, is mainly driven by dispersal limitation, environmental filtering, or species interaction. This calls for a holistic perspective involving both evolutionary processes and ecological dynamics, as provided by the unifying framework of the “metacommunity speciation model”.The current study used the species-rich model taxon Gastropoda to assess how extant communities in Lake Ohrid are structured by performing process-based metacommunity analyses. Specifically, the study aimed (1) to identifying the relative importance of the three community assembly processes and (2) to test whether the importance of these individual processes changes gradually with lake depth or discontinuously with eco-zone shifts.Based on automated eco-zone detection and process-specific simulation steps, we demonstrated that dispersal limitation had the strongest influence on gastropod community composition. However, it was not the exclusive assembly process, but acted together with the other two processes – environmental filtering and species interaction. The relative importance of the community assembly processes varied both with lake depth and eco-zones, though the processes were better predicted by the latter.This suggests that environmental characteristics have a pronounced effect on shaping gastropod communities via assembly processes. Moreover, the study corroborated the high importance of dispersal limitation for both maintaining species richness in Lake Ohrid (through its impact on community composition) and generating endemic biodiversity (via its influence on diversification processes). However, according to the metacommunity speciation model, the inferred importance of environmental filtering and biotic interaction also suggests a small but significant influence of ecological speciation. These findings contribute to the main goal of the Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) deep drilling initiative – inferring the drivers of biotic evolution – and might provide an integrative perspective on biological and limnological dynamics in ancient Lake Ohrid.

scholarly journals Deterministic Selection Dominates Microbial Community Assembly in Termite Mounds Across a Large Spatial Area

2020 ◽  
Author(s):  
Qing-Lin Chen ◽  
Hang-Wei Hu ◽  
Zhen-Zhen Yan ◽  
Chao-Yu Li ◽  
Bao-Anh Thi Nguyen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Stochastic Processes ◽  
Microbial Communities ◽  
Fungal Community ◽  
Community Assembly ◽  
Distance Decay ◽  
Termite Mounds ◽  
Deterministic Processes ◽  
Microbial Community Assembly

Abstract Background: Termites are ubiquitous insects in tropical and subtropical habitats, where they construct massive mounds from soil, their saliva and excreta. Termite mounds harbor an enormous amount of microbial inhabitants, which regulate multiple ecosystem functions such as mitigating methane emissions and increasing ecosystem resistance to climate change. However, we lack a mechanistic understanding about the role of termite mounds in modulating the microbial community assembly processes, which are essential to unravel the biological interactions of soil fauna and microorganisms, the major components of soil food webs. We conducted a large-scale survey across a >1500 km transect in northern Australia to investigate biogeographical patterns of bacterial and fungal community in 134 termite mounds and the relative importance of deterministic versus stochastic processes in microbial community assembly. Results: Microbial alpha (number of phylotypes) and beta (changes in bacterial and fungal community composition) significantly differed between termite mounds and surrounding soils. Microbial communities in termite mounds exhibited a significant distance-decay pattern, and fungal communities had a stronger distance-decay relationship (slope = -1.91) than bacteria (slope = -0.21). Based on the neutral community model (fitness < 0.7) and normalized stochasticity ratio index (NST) with a value below the 50% boundary point, deterministic selection, rather than stochastic forces, predominated the microbial community assembly in termite mounds. Deterministic processes exhibited significantly weaker impacts on bacteria (NST = 45.23%) than on fungi (NST = 33.72%), probably due to the wider habitat niche breadth and higher potential migration rate of bacteria. The abundance of antibiotic resistance genes (ARGs) was negatively correlated with bacterial/fungal biomass ratios, indicating that ARG content might be an important biotic factor that drove the biogeographic pattern of microbial communities in termite mounds. Conclusions: Deterministic processes play a more important role than stochastic processes in shaping the microbial community assembly in termite mounds, an unique habitat ubiquitously distributed in tropical and subtropical ecosystems. An improved understanding of the biogeographic patterns of microorganisms in termite mounds is crucial to decipher the role of soil faunal activities in shaping microbial community assembly, with implications for their mediated ecosystems functions and services.

scholarly journals Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity

2021 ◽  
Vol 12 ◽  
Author(s):  
Scott F. George ◽  
Noah Fierer ◽  
Joseph S. Levy ◽  
Byron Adams
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Vapor Flow ◽  
Arid Soils ◽  
Opposite Pattern ◽  
Dry Valley

Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.

Sign in / Sign up

Export Citation Format

Share Document