Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil

Critical steps in an environmental metaproteomics workflow

Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As the field is still maturing, it lacks consistent workflows, making it challenging for non-expert researchers to navigate. This review aims to introduce the workflow of environmental metaproteomics. It outlines the standard practices for sample collection, processing, and analysis, and offers strategies to overcome the unique challenges presented by common environmental matrices such as soil, freshwater, marine environments, biofilms, sludge, and symbionts. The review also highlights the bottlenecks in data analysis that are specific to metaproteomics samples and provides suggestions for researchers to obtain high-quality datasets. It includes recent benchmarking studies and descriptions of software packages specifically built for metaproteomics analysis. The article is written without assuming the reader's familiarity with single-organism proteomic workflows, making it accessible to those new to proteomics or mass spectrometry in general. This primer for environmental metaproteomics aims to improve accessibility to this exciting technology and empower researchers to tackle challenging and ambitious research questions. While it is primarily a resource for those new to the field, it should also be useful for established researchers looking to streamline or troubleshoot their metaproteomics experiments.

Identification of functional microflora underlying the biodegradation of sulfadiazine-contaminated substrates by Hermetia illucens

The increasing discharge of antibiotic residues into the natural environment, stemming from both human activities and animal farming, has detrimental effects on natural ecosystems and serves as a significant driving force for the spread of antibiotic resistance. Biodegradation is an important method for the elimination of antibiotics from contaminated substrates, but the identifying in situ microbial populations involved in antibiotic degradation is challenging. Here, DNA stable isotope probing (DNA-SIP) was employed to identify active sulfadiazine (SDZ) degrading microbes in the gut of black soldier fly larvae (BSFLs). At an initial SDZ concentration of 100 mg kg-1, the highest degradation efficiency reached 73.99% after 6 days at 28 °C. DNA-SIP revealed the incorporation of 13C6 from labeled SDZ in 9 genera, namely, Clostridum sensu stricto 1, Nesterenkonia, Bacillus, Halomonas, Dysgonomonas, Caldalkalibacillus, Enterococcus, g_unclassified_f_Xanthomonadaceae and g_unclassified_f_Micrococcaceae. Co-occurrence network analysis revealed that a significant positive correlation existed among SDZ degrading microbes in the gut microbiota, e.g., between Clostridium sensu stricto 1 and Nesterenkonia. Significant increases in carbohydrate metabolism, membrane transport and translation were crucial in the biodegradation of SDZ in the BSFL gut. These results elucidate the structure of SDZ-degrading microbial communities in the BSFL gut and in situ degradation mechanisms.

Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition

Climate change can alter the flow of nutrients and energy through terrestrial ecosystems. Using an inverse climate change field experiment in the central European Alps, we explored how long-term irrigation of a naturally drought-stressed pine forest altered the metabolic potential of the soil microbiome and its ability to decompose lignocellulolytic compounds as a critical ecosystem function. Drought mitigation by a decade of irrigation stimulated profound changes in the functional capacity encoded in the soil microbiome, revealing alterations in carbon and nitrogen metabolism as well as regulatory processes protecting microorganisms from starvation and desiccation. Despite the structural and functional shifts from oligotrophic to copiotrophic microbial lifestyles under irrigation and the observation that different microbial taxa were involved in the degradation of cellulose and lignin as determined by a time-series stable-isotope probing incubation experiment with 13C-labeled substrates, degradation rates of these compounds were not affected by different water availabilities. These findings provide new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a drought-prone pine forest and will help to improve our understanding of alterations in biogeochemical cycling under a changing climate.

Understory ferns promote the restoration of soil microbial diversity and function in previously degraded lands

Microorganisms facilitate the recovery of previously degraded soils, such as degraded lands experiencing vegetation restoration and understory expansion, through vital soil functions like nutrient cycling and decomposing organic matter. Despite the role of microorganisms in recovery, little is known about the effects of the process on microbial diversity and function. Here, we performed an understory fern, Dicranopteris dichotoma (Thunb.) Berhn removal treatments nested within three Masson pine (Pinus massoniana L.) plantations with different restoration years in subtropical China. Three ferns treatments including no ferns cover, with ferns cover, and the ferns removal treatments were established to assess the impact of the ferns on soil microbial diversity and function during revegetation and drivers of observed changes. We combined high-throughput sequencing, network structure modeling, and function prediction of soil bacterial and fungal communities to determine microbial diversity and functions. Our results showed that soil bacterial and fungal diversity increased with restoration time. Understory ferns significantly increased soil microbial diversity in the un-restored land but the effect became smaller in two restored sites. Understory ferns significantly increased the relative abundance of bacterial phyla Proteobacteria and Acidobacteria, but decreased that of Chloroflexi and Firmicutes. Furthermore, the presence of ferns increased the abundance of Basidiomycota, but increased the abundance of Ascomycota. Co-occurrence network analysis revealed that the presence of ferns leads to more complex of bacterial networks with more connections, nodes, average degrees, betweenness, and degrees. The functional predictions indicate that aerobic chemoheterotrophy, chemoheterotrophy, and nitrogen fixation functional groups play key roles in the nutrient cycling of soils with ferns cover. The bacterial and fungal community compositions were strongly affected by revegetation and understory ferns as litter biomass and soil nitrogen were identified as the key environmental factors. Our study highlights the role of understory in facilitating microbial diversity and function recovery during degraded lands restoration.

The Succession of the Cellulolytic Microbial Community from the Soil during Oat Straw Decomposition

The process of straw decomposition is dynamic and is accompanied by the succession of the microbial decomposing community, which is driven by poorly understood interactions between microorganisms. Soil is a complex ecological niche, and the soil microbiome can serve as a source of potentially active cellulolytic microorganisms. Here, we performed an experiment on the de novo colonization of oat straw by the soil microbial community by placing nylon bags with sterilized oat straw in the pots filled with chernozem soil and incubating them for 6 months. The aim was to investigate the changes in decomposer microbiota during this process using conventional sequencing techniques. The bacterial succession during straw decomposition occurred in three phases: the early phase (first month) was characterized by high microbial activity and low diversity, the middle phase (second to third month) was characterized by low activity and low diversity, and the late phase (fourth to sixth months) was characterized by low activity and high diversity. Analysis of amplicon sequencing data revealed three groups of co-changing phylotypes corresponding to these phases. The early active phase was abundant in the cellulolytic members from Pseudomonadota, Bacteroidota, Bacillota, and Actinobacteriota for bacteria and Ascomycota for fungi, and most of the primary phylotypes were gone by the end of the phase. The second intermediate phase was marked by the set of phylotypes from the same phyla persisting in the community. In the mature community of the late phase, apart from the core phylotypes, non-cellulolytic members from Bdellovibrionota, Myxococcota, Chloroflexota, and Thermoproteota appeared. Full metagenome sequencing of the microbial community from the end of the middle phase confirmed that major bacterial and fungal members of this consortium had genes of glycoside hydrolases (GH) connected to cellulose and chitin degradation. The real-time analysis of the selection of these genes showed that their representation varied between phases, and this occurred under the influence of the host, and not the GH family factor. Our findings demonstrate that soil microbial community may act as an efficient source of cellulolytic microorganisms and that colonization of the cellulolytic substrate occurs in several phases, each characterized by its own taxonomic and functional profile.

Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing

Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial dynamics in soil that govern carbon (C) cycling are not well understood. Life history strategies explain the complex dynamics of bacterial populations and activities based on trade-offs in energy allocation to growth, resource acquisition, and survival. Such trade-offs influence the fate of soil C, but their genomic basis remains poorly characterized. We used multisubstrate metagenomic DNA stable isotope probing to link genomic features of bacteria to their C acquisition and growth dynamics. We identify several genomic features associated with patterns of bacterial C acquisition and growth, notably genomic investment in resource acquisition and regulatory flexibility. Moreover, we identify genomic trade-offs defined by numbers of transcription factors, membrane transporters, and secreted products, which match predictions from life history theory. We further show that genomic investment in resource acquisition and regulatory flexibility can predict bacterial ecological strategies in soil. IMPORTANCE Soil microbes are major players in the global carbon cycle, yet we still have little understanding of how the carbon cycle operates in soil communities. A major limitation is that carbon metabolism lacks discrete functional genes that define carbon transformations. Instead, carbon transformations are governed by anabolic processes associated with growth, resource acquisition, and survival. We use metagenomic stable isotope probing to link genome information to microbial growth and carbon assimilation dynamics as they occur in soil. From these data, we identify genomic traits that can predict bacterial ecological strategies which define bacterial interactions with soil carbon.

Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

Soil microbiomes are sensitive to current and previous soil conditions, and bacterial 'bioindicators' of biological, physical, and chemical soil properties have considerable potential for soil health assessment. However, the lack of ecological or physiological information for most soil microorganisms limits our ability to interpret the associations of bioindicators and, thus, their utility for guiding management. We identified bioindicators of tillage intensity and twelve soil properties used to rate soil health using a 16S rRNA gene-based survey of farmland across North America. We then inferred the genomic traits of bioindicators and evaluated their environment-wide associations (EWAS) with respect to agricultural management practice, disturbance, and plant associations with 89 studies from agroecosystems. Most bioindicators were either positively correlated with biological properties (e.g., organic matter) or negatively correlated with physical and chemical properties. Higher soil health ratings corresponded with smaller genome size and higher coding density, while lower ratings corresponded with larger genomes and higher rrn copy number. Community-weighted genome size explained most variation in health ratings. EWAS linked prominent bioindicators with the impacts of environmental disturbances. Our findings provide ecological insights into bioindicators of soil properties relevant to soil health management, illustrating the tight coupling of microbiome and soil function.

Bacterial community shifts in a di-(2-ethylhexyl) phthalate-degrading enriched consortium and the isolation and characterization of degraders predicted through network analyses

Di-(2-ethylhexyl) phthalate (DEHP) is an extensively used and toxic phthalate plasticizer that is widely reported in marine environments. Degradation of DEHP by bacteria from several environments have been studied, but little is known about marine sediment bacteria that can degrade DEHP and other phthalate plasticizers. Therefore, in this study, we enriched a bacterial consortium C10 that can degrade four phthalate plasticizers of varying alkyl chain lengths (DEHP, dibutyl phthalate, diethyl phthalate, and dimethyl phthalate) from marine sediment. The major bacterial genera in C10 during degradation of the phthalate plasticizers were Glutamicibacter, Ochrobactrum, Pseudomonas, Bacillus, Stenotrophomonas, and Methylophaga. Growth of C10 on DEHP intermediates (mono-ethylhexyl phthalate, 2-ethylhexanol, phthalic acid, and protocatechuic acid) was studied and these intermediates enhanced the Brevibacterium, Ochrobactrum, Achromobacter, Bacillus, Sporosarcina, and Microbacterium populations. Using a network-based approach, we predicted that Bacillus, Stenotrophomonas, and Microbacterium interacted cooperatively and were the main degraders of phthalate plasticizers. Through selective isolation techniques, we obtained twenty isolates belonging to Bacillus, Microbacterium, Sporosarcina, Micrococcus, Ochrobactrum, Stenotrophomonas, Alcaligenes, and Cytobacillus. The best DEHP-degraders were Stenotrophomonas acidaminiphila OR13, Microbacterium esteraromaticum OR16, Sporosarcina sp. OR19, and Cytobacillus firmus OR20 (83.68%, 59.1%, 43.4%, and 40.6% degradation of 100 mg/L DEHP in 8 d), which agrees with the prediction of key degraders. This is the first report of DEHP degradation by all four bacteria and, thus, our findings reveal as yet unknown PAE-degradation capabilities of marine sediment bacteria. This study provides insights into how bacterial communities adapt to degrade or resist the toxicities of different PAEs and demonstrates a simple approach for the prediction and isolation of potential pollutant degraders from complex and dynamic bacterial communities.

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

BACKGROUND

Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing-SIP-remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling.

RESULTS

Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to ¹³C-AMF hyphosphere DNA from a ¹³CO₂ plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10-33 atom% ¹³C), even though the soils' overall enrichment was low (1.8 atom% ¹³C). We assembled 212 ¹³C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived ¹³C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera.

CONCLUSIONS

Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP-fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat-generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs' phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling. Video Abstract.

Tracing Carbon Metabolism with Stable Isotope Metabolomics Reveals the Legacy of Diverse Carbon Sources in Soil

Carbon metabolism in soil remains poorly described due to the inherent difficulty of obtaining information on the microbial metabolites produced by complex soil communities. Our study demonstrates the use of stable isotope probing (SIP) to study carbon metabolism in soil by tracking 13 C from supplied carbon sources into metabolite pools and biomass.

The Structure of Stable Cellulolytic Consortia Isolated from Natural Lignocellulosic Substrates

Recycling plant matter is one of the challenges facing humanity today and depends on efficient lignocellulose degradation. Although many bacterial strains from natural substrates demonstrate cellulolytic activities, the CAZymes (Carbohydrate-Active enZYmes) responsible for these activities are very diverse and usually distributed among different bacteria in one habitat. Thus, using microbial consortia can be a solution to rapid and effective decomposition of plant biomass. Four cellulolytic consortia were isolated from enrichment cultures from composting natural lignocellulosic substrates—oat straw, pine sawdust, and birch leaf litter. Enrichment cultures facilitated growth of similar, but not identical cellulose-decomposing bacteria from different substrates. Major components in all consortia were from Proteobacteria, Actinobacteriota and Bacteroidota, but some were specific for different substrates—Verrucomicrobiota and Myxococcota from straw, Planctomycetota from sawdust and Firmicutes from leaf litter. While most members of the consortia were involved in the lignocellulose degradation, some demonstrated additional metabolic activities. Consortia did not differ in the composition of CAZymes genes, but rather in axillary functions, such as ABC-transporters and two-component systems, usually taxon-specific and associated with CAZymes. Our findings show that enrichment cultures can provide reproducible cellulolytic consortia from various lignocellulosic substrates, the stability of which is ensured by tight microbial relations between its components.

Bacterial community dynamics explain carbon mineralization and assimilation in soils of different land-use history

Soil dwelling microorganisms are key players in the terrestrial carbon cycle, driving both the degradation and stabilization of soil organic matter. Bacterial community structure and function vary with respect to land-use, yet the ecological drivers of this variation remain poorly described and difficult to predict. We conducted a multi-substrate DNA-stable isotope probing experiment across cropland, old-field, and forest habitats to link carbon mineralization dynamics with the dynamics of bacterial growth and carbon assimilation. We tracked the movement of ¹³ C derived from five distinct carbon sources as it was assimilated into bacterial DNA over time. We show that carbon mineralization, community composition, and carbon assimilation dynamics all differed with respect to land-use. We also show that microbial community dynamics affect carbon assimilation dynamics and are associated with soil DNA content. Soil DNA yield is easy to measure and may be useful in predicting microbial community dynamics linked to soil carbon cycling. This article is protected by copyright. All rights reserved.

Conditional filamentation as an adaptive trait of bacteria and its ecological significance in soils

Bacteria can regulate cell morphology in response to environmental conditions, altering their physiological and metabolic characteristics to improve survival. Conditional filamentation, in which cells suspend division while continuing lateral growth, is a strategy with a range of adaptive benefits. Here, we review the causes and consequences of conditional filamentation with respect to bacterial physiology, ecology and evolution. We describe four major benefits from conditional filamentation: stress tolerance, surface colonization, gradient spanning and the facilitation of biotic interactions. Adopting a filamentous growth habit involves fitness trade-offs which are also examined. We focus on the role of conditional filamentation in soil habitats, where filamentous morphotypes are highly prevalent and where environmental heterogeneity can benefit a conditional response. To illustrate the use of information presented in our review, we tested the conditions regulating filamentation by the forest soil isolate Paraburkholderia elongata 5N^T . Filamentation by P. elongata was induced at elevated phosphate concentrations, and was associated with the accumulation of intracellular polyphosphate, highlighting the role of filamentation in a phosphate-solubilizing bacterium. Conditional filamentation enables bacteria to optimize their growth and metabolism in environments that are highly variable, a trait that can impact succession, symbioses, and biogeochemistry in soil environments.

Community RNA-Seq: multi-kingdom responses to living versus decaying roots in soil

Roots are a primary source of organic carbon input in most soils. The consumption of living and detrital root inputs involves multi-trophic processes and multiple kingdoms of microbial life, but typical microbial ecology studies focus on only one or two major lineages. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis ("community RNA-Seq") and simultaneously assess the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in 13CO2-labeled microcosms amended with 15N-root litter to identify the preferences of rhizosphere organisms for root exudates (13C) versus decaying root biomass (15N) using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group's more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving complex interactions, and our methodology can be used to track the trajectory of carbon through multi-kingdom soil food webs.