scholarly journals Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nanette C. Raczka ◽  
Juan Piñeiro ◽  
Malak M. Tfaily ◽  
Rosalie K. Chu ◽  
Mary S. Lipton ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Arbuscular Mycorrhizal ◽  
Stable Isotope Probing ◽  
Microbial Competition ◽  
Microbial Decomposition ◽  
Important Interaction ◽  
Metabolic Products ◽  
Ecosystem Level ◽  
Microbial Products ◽  
And Function

AbstractMicrobial decomposition drives the transformation of plant-derived substrates into microbial products that form stable soil organic matter (SOM). Recent theories have posited that decomposition depends on an interaction between SOM chemistry with microbial diversity and resulting function (e.g., enzymatic capabilities, growth rates). Here, we explicitly test these theories by coupling quantitative stable isotope probing and metabolomics to track the fate of 13C enriched substrates that vary in chemical composition as they are assimilated by microbes and transformed into new metabolic products in soil. We found that differences in forest nutrient economies (e.g., nutrient cycling, microbial competition) led to arbuscular mycorrhizal (AM) soils harboring greater diversity of fungi and bacteria than ectomycorrhizal (ECM) soils. When incubated with 13C enriched substrates, substrate type drove shifts in which species were active decomposers and the abundance of metabolic products that were reduced or saturated in the highly diverse AM soils. The decomposition pathways were more static in the less diverse, ECM soil. Importantly, the majority of these shifts were driven by taxa only present in the AM soil suggesting a strong link between microbial identity and their ability to decompose and assimilate substrates. Collectively, these results highlight an important interaction between ecosystem-level processes and microbial diversity; whereby the identity and function of active decomposers impacts the composition of decomposition products that can form stable SOM.

Raczka et al. Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil.

2021 ◽  
Author(s):  
Juan Piñeiro ◽  
Nanette Raczka ◽  
Ember Morrissey ◽  
Edward Brzostek ◽  
Mary Lipton ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Arbuscular Mycorrhizal ◽  
Stable Isotope Probing ◽  
Microbial Competition ◽  
Microbial Decomposition ◽  
Soil P ◽  
Important Interaction ◽  
Metabolic Products ◽  
Ecosystem Level ◽  
And Function

Microbial decomposition drives the transformation of plant-derived substrates into microbial products that form stable soil organic matter (SOM). Recent theories have posited that decomposition depends on an interaction between SOM chemistry with microbial diversity and resulting function. Here, we explicitly test these theories by coupling quantitative stable isotope probing and metabolomics to track the fate of 13C labeled substrates that vary in chemical composition as they are assimilated by microbes and transformed into new metabolic products in the lab. We found that mycorrhizal-driven differences in forest nutrient economies (e.g., nutrient cycling, microbial competition) led to arbuscular mycorrhizal (AM) soils harboring greater microbial diversity than ectomycorrhizal (ECM) soils. When incubated with 13C labeled substrates, the greater diversity in AM soils led to substrate type driving shifts in the identity of active decomposers and their metabolic products. The decomposition pathways were more static in the less diverse, ECM soil. Importantly, the majority of these shifts were driven by non-co-occurring taxa suggesting a strong link between microbial identity and specialized function. Collectively, these results highlight an important interaction between ecosystem-level processes and microbial diversity; whereby the identity and function of active decomposers impacts the composition of decomposition products that can form stable SOM.

Ecosystems processes

2018 ◽  
Author(s):  
Karen J. Esler ◽  
Anna L. Jacobsen ◽  
R. Brandon Pratt
Keyword(s):  
Ecosystem Function ◽  
Mineral Nutrients ◽  
Structure And Function ◽  
Water Dynamics ◽  
Ecosystem Level ◽  
Key Drivers ◽  
And Function ◽  
Mediterranean Type Ecosystems

Ecosystems are assemblages of organisms interacting with one another and their environment (Chapter 1). Key to the functioning of ecosystems is the flow of energy, carbon, mineral nutrients, and water in these systems. The numerous processes involved are chiefly driven by climate, soil, and fire (Chapter 2). In cases where the key drivers are the same in different areas, then ecosystems should converge in their structure and function, which has been a motivation for comparing across mediterranean-type climate (MTC) regions. Convergence of MTC regions has been evaluated, but such comparisons at the ecosystem level are challenging because ecosystems are complex and dynamic entities. Here we review carbon, nutrient, and water dynamics of mediterranean-type ecosystems in the context of ecosystem function. As nutrients in soils are low in some MTC regions, we review how this has led to unique adaptations to meet this challenge.

scholarly journals A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils

2021 ◽  
Vol 22 (7) ◽  
pp. 3438
Author(s):  
Juan Liu ◽  
Xiangwei He ◽  
Jingya Sun ◽  
Yuchao Ma
Keyword(s):  
Soil Fertility ◽  
Microbial Diversity ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Antibiotics Resistance ◽  
Plant Growth Promoting Bacteria ◽  
Soil Microbial Diversity ◽  
Antibiotic Target ◽  
And Function

Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.

scholarly journals Longitudinal sampling of external mucosae in farmed European seabass reveals the impact of water temperature on bacterial dynamics

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Daniela Rosado ◽  
Raquel Xavier ◽  
Jo Cable ◽  
Ricardo Severino ◽  
Pedro Tarroso ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Microbial Diversity ◽  
Water Temperature ◽  
Abiotic Factors ◽  
Seasonal Effect ◽  
Microbial Composition ◽  
Surrounding Water ◽  
European Seabass ◽  
And Function ◽  
The Impact

AbstractFish microbiota are intrinsically linked to health and fitness, but they are highly variable and influenced by both biotic and abiotic factors. Water temperature particularly limits bacterial adhesion and growth, impacting microbial diversity and bacterial infections on the skin and gills. Aquaculture is heavily affected by infectious diseases, especially in warmer months, and industry practices often promote stress and microbial dysbiosis, leading to an increased abundance of potentially pathogenic bacteria. In this regard, fish mucosa health is extremely important because it provides a primary barrier against pathogens. We used 16 rRNA V4 metataxonomics to characterize the skin and gill microbiota of the European seabass, Dicentrarchus labrax, and the surrounding water over 12 months, assessing the impact of water temperature on microbial diversity and function. We show that the microbiota of external mucosae are highly dynamic with consistent longitudinal trends in taxon diversity. Several potentially pathogenic genera (Aliivibrio, Photobacterium, Pseudomonas, and Vibrio) were highly abundant, showing complex interactions with other bacterial genera, some of which with recognized probiotic activity, and were also significantly impacted by changes in temperature. The surrounding water temperature influenced fish microbial composition, structure and function over time (days and months). Additionally, dysbiosis was more frequent in warmer months and during transitions between cold/warm months. We also detected a strong seasonal effect in the fish microbiota, which is likely to result from the compound action of several unmeasured environmental factors (e.g., pH, nutrient availability) beyond temperature. Our results highlight the importance of performing longitudinal studies to assess the impact of environmental factors on fish microbiotas.

scholarly journals Carbohydrate complexity structures stable diversity in gut-derived microbial consortia under high dilution pressure

2020 ◽  
Author(s):  
Tianming Yao ◽  
Ming-Hsu Chen ◽  
Stephen R. Lindemann
Keyword(s):  
Microbial Diversity ◽  
Structural Complexity ◽  
Structure And Function ◽  
Microbial Consortia ◽  
Carbohydrate Structure ◽  
High Dilution ◽  
Chemical Complexity ◽  
Metabolic Interactions ◽  
And Function

ABSTRACTDietary fibers are major substrates for the colonic microbiota, but the structural specificity of these fibers for the diversity, structure, and function of gut microbial communities are poorly understood. Here, we employed an in vitro sequential batch fecal culture approach to determine: 1) whether the chemical complexity of a carbohydrate structure influences its ability to maintain microbial diversity in the face of high dilution pressure and 2) whether substrate structuring or obligate microbe-microbe metabolic interactions (e.g. exchange of amino acids or vitamins) exert more influence on maintained diversity. Sorghum arabinoxylan (SAX, complex polysaccharide), inulin (low-complexity oligosaccharide) and their corresponding monosaccharide controls were selected as model carbohydrates. Our results demonstrate that complex carbohydrates stably sustain diverse microbial consortia. Further, very similar final consortia were enriched on SAX from the same individual’s fecal microbiota across a one-month interval, suggesting that polysaccharide structure is more influential than stochastic alterations in microbiome composition in governing the outcomes of sequential batch cultivation experiments. SAX-consuming consortia were anchored by Bacteroides ovatus and retained diverse consortia of >12 OTUs; whereas final inulin-consuming consortia were dominated either by Klebsiella pneumoniae or Bifidobacterium sp. and Escherichia coli. Furthermore, auxotrophic interactions were less influential in structuring microbial consortia consuming SAX than the less-complex inulin. These data suggest that carbohydrate structural complexity affords independent niches that structure fermenting microbial consortia, whereas other metabolic interactions govern the composition of communities fermenting simpler carbohydrates.IMPORTANCEThe mechanisms by which gut microorganisms compete for and cooperate on human-indigestible carbohydrates of varying structural complexity remain unclear. Gaps in this understanding make it challenging to predict the effect of a particular dietary fiber’s structure on the diversity, composition, or function of gut microbiomes, especially with inter-individual variability in diets and microbiomes. Here, we demonstrate that carbohydrate structure governs the diversity of gut microbiota under high dilution pressure, suggesting that such structures may support microbial diversity in vivo. Further, we also demonstrate that carbohydrate polymers are not equivalent in the strength by which they influence community structure and function, and that metabolic interactions among members arising due to auxotrophy exert significant influence on the outcomes of these competitions for simpler polymers. Collectively, these data suggest that large, complex dietary fiber polysaccharides structure the human gut ecosystem in ways that smaller and simpler ones may not.

scholarly journals Microbial Diversity and Function in Shallow Subsurface Sediment and Oceanic Lithosphere of the Atlantis Massif

mBio ◽  
2021 ◽  
Author(s):  
J. Goordial ◽  
T. D’Angelo ◽  
J. M. Labonté ◽  
N. J. Poulton ◽  
J. M. Brown ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Oceanic Lithosphere ◽  
Global Scale ◽  
Nutrient Cycles ◽  
Subsurface Sediment ◽  
Shallow Subsurface ◽  
Low Concentrations ◽  
Atlantis Massif ◽  
And Function

The subsurface rock beneath the ocean is one of the largest biospheres on Earth, and microorganisms within influence global-scale nutrient cycles. This biosphere is difficult to study, in part due to the low concentrations of microorganisms that inhabit the vast volume of the marine lithosphere.

Inhibition of Mold Growth and Aflatoxin Production by Lactobacillus spp1

1990 ◽  
Vol 53 (3) ◽  
pp. 230-236 ◽  
Author(s):  
ANJANI KARUNARATNE ◽  
ELENORA WEZENBERG ◽  
LLOYD B. BULLERMAN
Keyword(s):  
Lactobacillus Acidophilus ◽  
Ph Effect ◽  
Aflatoxin Production ◽  
Individual Species ◽  
Mold Growth ◽  
Microbial Competition ◽  
Growing Cell ◽  
Metabolic Products ◽  
Different Strains ◽  
Silage Inoculant

The effect of three individual species of lactobacilli (Lactobacillus acidophilus, L. bulgaricus, and L. plantarum) and a commercial silage inoculant, containing three different strains of the same species, on growth and aflatoxin production of A. flavus subsp. parasiticus NRRL 2999 was determined. The study was done in three substrates; a liquid semi-synthetic broth, rice, and corn. The effect of the growing cell masses of the lactobacilli as well as the effect of metabolic products contained in cell free filtrates were determined in the liquid medium. The cells were effective in preventing growth of the mold, and bacterial metabolites were effective in reducing the amount of aflatoxin produced, although growth was not affected. The prevention of growth that was observed was determined to be relative to a pH effect and microbial competition; however, the lower levels of aflatoxin obtained in the presence of cell free supernatant culture fluids could not be explained on the basis of pH or competition. Mold growth was not affected by the presence of the silage inoculant on the rice and corn. However, increased levels of aflatoxin B1 were observed in the presence of the silage inoculant on rice, and decreased levels of aflatoxin G1 were observed on the presence of the silage inoculant on corn.

Species Interactions in Percid Communities

1977 ◽  
Vol 34 (10) ◽  
pp. 1941-1951 ◽  
Author(s):  
James MacLean ◽  
John J. Magnuson
Keyword(s):  
Species Interactions ◽  
Resource Partitioning ◽  
Cold Water ◽  
Time Of Day ◽  
Thermal Habitat ◽  
Stratified Lakes ◽  
Thermal Requirements ◽  
Important Interaction ◽  
Manipulative Experiments ◽  
And Function

Evidence for species interactions in communities with Perca and Stizostedion is evaluated. Substantial evidence exists for the importance of predation by and on percids to community structure and function. Some evidence also clearly demonstrates that competition is an important interaction both within Perca populations and between Perca and other species. The necessity of using manipulative experiments to test for community level effects of competition and predation is emphasized. Such manipulative experiments, however, should be restricted in number and conducted with great care, because the community changes they induce are often irreversible and detrimental.Species interactions related to feeding have apparently resulted in the partitioning of habitat and food resources among fishes in percid communities. Partitioning of space is considered in terms of distribution of Perca and Stizostedion in respect to temperature in stratified and unstratified aquatic systems. In stratified lakes, percids are expected to be spatially segregated from fishes with other thermal requirements, such as the warmwater centrarchids and the cold-water salmonids. Seasons and depths of potentially intense interactions are diagrammed. In unstratified lakes, latitude and lake size set the stage for the thermal habitat that favors the physiology of percids in some systems. Resource partitioning, in respect to food size and time of day for foraging, is also diagrammed and appears to be important. It is argued that species interactions between other fishes and Perca and Stizostedion are greatly reduced by present patterns of resource utilization. Key words: competition, predation, resource partitioning, percid communities

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