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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Litter chemistry influences decomposition through activity of specific microbial functional guilds

Abstract Niche differentiation among species is a key mechanism by which biodiversity may be linked to ecosystem function. We tested a set of widely invoked hypotheses about the extent of niche differentiation in one of the most diverse communities on Earth, decomposer microorganisms, by measuring their response to changes in three abundant litter resources: lignin, cellulose, and nitrogen (N). To do this, we used the model system Arabidopsis thaliana to manipulate lignin, cellulose, and N availability and then used high‐throughput sequencing to measure the response of microbial communities during decay. Resequencing the decomposer communities after incubation of decomposed litter with pure substrates showed that groups of species had unique substrate use profiles, such that species organized into functional “guilds” of decomposers that were associated with individual litter chemicals. Low concentrations of lignin, cellulose, or N in the litter caused unique shifts in decomposer community composition after 1 yr of decay. Low cellulose plants had low levels of fungi in all decomposer guilds, low lignin plants had high levels of fungi in all decomposer guilds, and low N plants had low levels of fungi in decomposer guilds associated with sucrose and lignin. The relative abundance of decomposer guilds correlated with the total loss of individual litter chemicals during litter decay in the field. In addition, N fertilization shifted decomposer communities during both the early and later stages of decay to those dominated by decomposers in the cellulose guild. Our results contrast the assumption that major carbon (C) and N degradation mechanisms are uniform across whole decomposer communities and instead suggest that decomposition arises from complementarity among groups of metabolically distinct taxa.

Bhatnagar, Jennifer M.↗
DOE OSTI2024

Switchgrass ( Panicum virgatum L.) cultivars have similar impacts on soil carbon and nitrogen stocks and microbial function

Abstract Switchgrass ( Panicum virgatum L.) production for biofuel has the potential to produce reasonable yields on lands not suited for conventional agriculture. We assessed nine switchgrass cultivars representing lowland and upland ecotypes grown for 11 years at a site in the upper Midwest USA for belowground differences in soil carbon and nitrogen stocks, soil organic matter fractions, and standing root biomass to 1 m depth. We also compared potential nitrogen mineralization and carbon substrate use through community‐level physiological profiling in surface soils (0–10 cm depth). Average yields and standing root biomass differed among cultivars and between ecotypes, but we found no significant cultivar‐related impacts on soil carbon and nitrogen stocks, on the distribution of particulate and mineral‐associated soil organic matter fractions, nor on potential nitrogen mineralization or microbial community‐level physiological profiles. That these traits did not differ among cultivars suggests that soil carbon and nitrogen gains under switchgrass are likely to be robust with respect to cultivar differences, and to this point not much affected by breeding efforts.

Agriculture↗
DOE OSTI2016

Zinc concentration affects the functional groups of microbial communities in sugarcane-cultivated soil

The addition of zinc (Zn) to the soil has significant gains in sugarcane productivity. The understanding of the consequences of zinc application requires insight into ecological aspects of changes in soil microbial communities. Here, we evaluated the effects of zinc application on richness, diversity, evenness and structure of microbial functional genes in sugarcane-cultivated soil, and response thresholds of abundance for groups of microbial functional genes on different zinc concentrations added to the soil (0, 5, 10 and 20 kg Zn ha -1 ) in two sugarcane fields in the Northeastern São Paulo state, Brazil. Using a high-density functional gene array termed GeoChip 5.0, which contains 101,796 distinct probes belonging to gene categories involved in zinc transport, secondary metabolism, stress, virulence and nutrient cycling, differences were observed in the functional gene structure of microbial communities and abundance of specific gene families with a threshold between 5 and 10 kg Zn ha -1 . However, the richness, diversity and evenness of functional genes did not differ across the zinc gradients in soil. Cluster analysis based on microbial functional subcategories revealed variation in abundances across the gradient of zinc concentrations in soil mainly for virulence, stress, secondary metabolism, and carbon- and phosphorus-cycling-related gene families. A threshold in abundance was observed between 5 and 10 kg Zn ha -1 with high abundance of microbial gene families associated with zinc transporter proteins, antioxidant enzymes, exoenzymes associated with infection, secretion proteins, virulence regulatory genes, carbon fixation, and phosphorus utilization in soils supplemented with up to 5 kg Zn ha -1 . In these same soils, reduced abundance was observed for gene families associated with methanogenesis, metabolism of halogen and carotenoid, and antiphagocytosis compared with soil supplements with 10 or 20 kg Zn ha -1 . The results suggest that changes in microbial functional gene structure and abundance could be used to evaluate the impact of soil management practices on soil microbial communities in sugarcane production fields.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition

Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. Yet, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, showing that field simulation was reliable. Soil microbial communities were altered ( p < .039) by both soil erosion and deposition, with dramatic increase in Cyanobacteria related to increased stability in soil aggregates. amyA genes encoding α-amylases were specifically increased ( p = .01) by soil deposition and positively correlated ( p = .02) to DOC, which likely explained changes in DOC. Surprisingly, most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or unaltered by both erosion and deposition, probably arising from acceleration of organic matter mineralization. These divergent responses support the necessity to include microbial components in evaluating ecological consequences. Moreover, Mantel tests showed strong, significant correlations between soil nutrients and functional structure but not taxonomic structure, demonstrating close relevance of microbial function traits to nutrient cycling.

16S rRNA sequencing↗
DOE OSTI2021

Macroecological distributions of gene variants highlight the functional organization of soil microbial systems

Abstract The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Determining Microbial Roles in Ecosystem Function: Redefining Microbial Food Webs and Transcending Kingdom Barriers

Microorganisms can have a profound and varying effect on the chemical character of environments and, thereby, ecological health. Their capacity to consume or transform contaminants leads to contrasting outcomes, such as the dissipation of nutrient pollution via denitrification, the breakdown of spilled oil, or eutrophication via primary producer overgrowth. Recovering the genomes of organisms directly from the environment is useful to gain insights into resource usage, interspecies collaborations (producers and consumers), and trait acquisition. Microbial data can also be considered alongside the broader biological character of an environment through the co-recovery of eukaryotic DNA. The contributions of individual microorganisms (bacteria, archaea, and protists) to snapshots of ecosystem processes can be determined by integrating genomics with functional methods. This combined approach enables a detailed understanding of how microbial communities drive biogeochemical cycles, and although currently limited by scale, key attributes can be effectively extrapolated with lower-resolution methods to determine wider ecological relevance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Evidence for a genetic basis in functional trait tradeoffs with microbial growth rate but not growth yield

Tradeoffs in microbial functional traits have been a focus of recently described ecological frameworks and of mathematical models of microbial community functioning. Tradeoffs in key traits such as growth rate, growth yield, resource acquisition, and stress tolerance may have either a genetic basis or a physiological basis, and the type of tradeoff can inform how traits are modeled and measured. Here we provide evidence that growth rate/decomposition and growth rate/stress tolerance tradeoffs have a primarily genetic basis in a phylogenetically diverse suite of ten leaf litter-inhabiting fungi. In contrast, growth yield tradeoffs with functional traits are more likely to have a physiological basis. Consideration of the type of tradeoff, genetic or physiological, should help to inform efforts to model microbial contributions to ecosystem processes, especially when considering different scales. Consideration of physiological tradeoffs may be important for understanding short-term variability (e.g., pulse events) and fine spatial scales, whereas genetic tradeoffs are likely to be useful for understanding regional- to continental-scale and medium- to long-term contributions of microbes to ecosystem processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Functional Enzyme-Based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics

The kinetics of biogeochemical processes in natural and engineered environmental systems are typically described using Monod-type or modified Monod-type models. These models rely on biomass as surrogates for functional enzymes in microbial community that catalyze biogeochemical reactions. A major challenge to apply such models is the difficulty to quantitatively measure functional biomass for constraining and validating the models. On the other hand, omics-based approaches have been increasingly used to characterize microbial community structure, functions, and metabolites. Here we proposed an enzyme-based model that can incorporate omics-data to link microbial community functions with biogeochemical process kinetics. The model treats enzymes as time-variable catalysts for biogeochemical reactions and applies biogeochemical reaction network to incorporate intermediate metabolites. The sequences of genes and proteins from metagenomes, as well as those from the UniProt database, were used for targeted enzyme quantification and to provide insights into the dynamic linkage among functional genes, enzymes, and metabolites that are necessary to be incorporated in the model. The application of the model was demonstrated using denitrification as an example by comparing model-simulated with measured functional enzymes, genes, denitrification substrates and intermediates

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Scale dependence in functional equivalence and difference in the soil microbiome

Climatic history can shape the functioning of soil microbial communities and thus rates of ecosystem processes such as organic matter decomposition. For example, broad spatial scale differences in climatic history, such as contrasting precipitation regimes, have been shown to generate unique microbial functional responses to contemporary moisture conditions. Yet it is an open question as to whether local differences in soil microclimate similarly influence the functional potential of decomposer communities. Here, we use a multi-scale approach within and among two temperate forest field sites to investigate this question. Soils from fifty-four microsites, that vary in their soil moisture climate-regimes, were used as inocula for a common leaf litter (Quercus rubra L.) in a controlled, laboratory microcosm study. Microcosms were placed under dry, mesic and wet lab-moisture conditions and the rate of carbon (C) mineralization of the litter was measured over 202 days. Our results reveal differences in decomposition rates under controlled conditions that highlight broad-scale functional differences between the soil communities at each site. Specifically, we found that C mineralization differed by as much as two-fold for soil communities when compared between the sites. Our results also show that functional differences of soil communities are observable within one site but not the other. In the site where local-scale functional legacies were apparent, the historical soil moisture microclimate-regimes generated as much as an 89% change in C mineralization rates of the leaf litter under the same contemporary, lab-imposed moisture conditions. Here, a similar pattern was not observable in the other site; instead, laboratory moisture conditions explained almost all variation in C mineralization. Notably, for the site with pronounced local-scale functional legacies, there was much greater within-site variation in field-soil microsite moisture than at the site which did not exhibit functional legacies, suggesting that the extent of local-scale variation in microclimate may act as control on whether local-scale functional legacies are observed. Regardless of whether this mechanism does explain our findings, our observations do confirm those from prior studies where regional-scale moisture-regime differences shape microbial function, and extend this prior work by providing evidence that pronounced local-scale differences in soil moisture microclimate-regimes are associated with microbial functional legacies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater

Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO 4 2- , NH 4 + or CH 4 concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO 4 2- , NH 4 + , oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO 4 2- , ORP, and high NH 4 + , as well as SO 4 2- and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling.

59 BASIC BIOLOGICAL SCIENCES↗