Understanding how microbiomes influence the systems they inhabit

Comprehensive analysis of the metabolism of core microorganisms in polyphenolic compound formation during the acetic acid fermentation stage of millet vinegar

BACKGROUND

Polyphenolic compounds in millet vinegar are crucial functional substances, but the mechanisms underlying their formation and metabolism remain unclear. Acetic acid fermentation (AAF) represents the most active microbial metabolism stage and is pivotal for forming polyphenolic compounds. This study comprehensively analyzed the role of the microbiome in polyphenolic compound production and metabolism during AAF.

RESULTS

Changing patterns were observed in both the microbiome and polyphenolic monomer compounds during AAF of millet vinegar. Lactobacillus harbinensis (0.624-0.454%) was identified as the dominant species in the pre-AAF stage, exhibiting a significant positive correlation with caffeic acid, kaempferic acid and kaempferolide (P < 0.05). Lactobacillus harbinensis-mediated polyphenolic compound metabolism was further confirmed through genomic analysis and pure culture fermentation techniques. Lactobacillus harbinensis encodes enzymes such as carbohydrate hydrolases, glycosidases and cellulases, which promote the release and metabolism of polyphenolic compounds from grain hulls.

CONCLUSION

This study confirmed that L. harbinensis, as a core microorganism in millet vinegar fermentation, can significantly augment the content of total phenols and specific polyphenolic compounds. These findings provide valuable insights for optimizing millet vinegar production. © 2024 Society of Chemical Industry.

Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation

Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, and soil connectivity. However, accurately representing the soil environment and establishing a tractable microbial community that limits confounding variables is difficult. Here, we use a reduced-complexity microbial consortium grown in a glass bead porous media amended with chitin to test the effects of moisture and a structural matrix on microbial phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, and metabolomes, we saw that our porous media system significantly altered microbial phenotypes compared with the liquid incubations, denoting the importance of incorporating pores and surfaces for understanding microbial phenotypes in soils. These phenotypic shifts were mainly driven by differences in expression of Streptomyces and Ensifer, which included a significant decrease in overall chitin degradation between porous media and liquid. Our findings suggest that the success of Ensifer in porous media is likely related to its ability to repurpose carbon via the glyoxylate shunt amidst a lack of chitin degradation byproducts while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits expressed by Ensifer and others, including motility, stress resistance, and carbon conservation, that likely influence the metabolic profiles observed across treatments. Together, these results demonstrate that porous media incubations promote structure-induced microbial phenotypes and are likely a better proxy for soil conditions than liquid culture systems. Furthermore, they emphasize that microbial phenotypes encompass not only the multi-enzyme pathways involved in metabolism but also include the complex interactions with the environment and other community members.IMPORTANCESoil moisture and porosity are critical in shaping microbial metabolism. However, accurately representing the soil environment in tractable laboratory experiments remains a challenging frontier. Through our reduced complexity microbial consortium experiment in porous media, we reveal that predicting microbial metabolism from gene-based pathways alone often falls short of capturing the intricate phenotypes driven by cellular interactions. Our findings highlight that porosity and moisture significantly affect chitin decomposition, with environmental matrix (i.e., glass beads) shifting community metabolism towards stress tolerance, reduced resource acquisition, and increased carbon conservation, ultimately invoking unique microbial strategies not evident in liquid cultures. Moreover, we find evidence that changes in moisture relate to community shifts regarding motility, transporters, and biofilm formation, which likely influence chitin degradation. Ultimately, our incubations showcase how reduced complexity communities can be informative of microbial metabolism and present a useful alternative to liquid cultures for studying soil microbial phenotypes.

Comparing field and lab quantitative stable isotope probing for nitrogen assimilation in soil microbes

Soil microbial communities play crucial roles in nutrient cycling and can help retain nitrogen in agricultural soils. Quantitative stable isotope probing (qSIP) is a useful method for investigating taxon-specific microbial growth and utilization of specific nutrients, such as nitrogen (N). Typically, qSIP is performed in a highly controlled lab setting, so the field relevance of lab qSIP studies remains unknown. We conducted and compared tandem lab and field qSIP to quantify the assimilation of 15N by maize-associated soil prokaryotic communities at two agricultural sites. Here, we show that field qSIP with 15N can be used to measure taxon-specific microbial N assimilation. Relative 15N assimilation rates were generally lower in the field, and the magnitude of this difference varied by site. Rates differed by method (lab vs field) for 19% of the top N assimilating genera. The field and lab measures were more comparable when relative assimilation rates were weighted by relative abundance to estimate the proportion of N assimilated by each genus with only ~10% of taxa differing by method. Of those that differed, the taxa consistently higher in the lab were inclined to have opportunistic lifestyle strategies, whereas those higher in the field had niches reliant on plant roots or in-tact soil structure (biofilms, mycelia). This study demonstrates that 15N-qSIP can be successfully performed using field-incubated soils to identify microbial allies in N retention and highlights the strengths and limitations of field and lab qSIP approaches.

IMPORTANCE

Soil microbes are responsible for critical biogeochemical processes in natural and agricultural ecosystems. Despite their importance, the functional traits of most soil organisms remain woefully under-characterized, limiting our ability to understand how microbial populations influence the transformation of elements such as nitrogen (N) in soil. Quantitative stable isotope probing (qSIP) is a powerful tool to measure the traits of individual taxa. This method has rarely been applied in the field or with 15N to measure nitrogen assimilation. In this study, we measured genus-specific microbial nitrogen assimilation in two agricultural soils and compared field and lab 15N qSIP methods. Our results identify taxa important for nitrogen assimilation in agricultural soils, shed light on the field relevance of lab qSIP studies, and provide guidance for the future application of qSIP to measure microbial traits in the field.

Functional characteristics and mechanisms of microbial community succession and assembly in a long-term moving bed biofilm reactor treating real municipal wastewater

Moving bed biofilm reactor (MBBR) technology with diverse merits is efficient in treating various waste streams whereas their microbial functional properties and ecology still need in-depth investigation, especially in real wastewater treatment systems. Herein, a well-controlled MBBR treating municipal wastewater was established to investigate the long-term system performance and the underlying principles of community succession and assembly. The system successfully achieved ammonium, TN, and chemical oxygen demand (COD) removal of 96.7 ± 2.2%, 75.2 ± 3.6%, and 90.3 ± 3.8%, respectively, under simplified operation and low energy consumption. The effluent TN concentrations achieved 6.2 ± 1.6 mg-N/L despite the influent fluctuations. Diverse functional denitrifiers, such as Denitratisoma, Thermomonas, and Flavobacterium, and the anammox bacteria Candidatus Brocadia successfully enriched in anoxic chamber biofilms. The nitrifiers Nitrosomonas (∼0.73%) and Nitrospira (∼14.0%) exhibited appreciable nitrification capacity in specialized aerobic chambers. Ecological null model and network analysis revealed that microbial community assembly was mainly regulated by niche-based deterministic processes and air diffusion in the aerobic chamber resulted in more intense and complex bacterial interactions. Environmental filters including influent substrate and operating conditions (e.g., reactor configuration, DO, and temperature) greatly shaped the microbial community structure and affected carbon and nitrogen metabolism. The positive ecological roles of influent microflora and functional redundancy in biofilm communities were believed to facilitate functional stability. The anammox process coupled with partial denitrification in a specialized chamber demonstrated positive application implications. These findings provided valuable perspectives in deciphering the microbiological and ecological mechanisms, functional properties, and application potentials of MBBR.

Phosphorus speciation in the hyporheic zone and its response to sediment-water quality-biological activity coupling effect

Different speciation of phosphorus in the hyporheic zone exhibit various release potentials, so as to control the phosphorus content in the overlying water. The process of phosphorus release under the multi-factor coupling of rivers is crucial for understanding the element cycle in complex environments. In this paper, the Weihe River in China was used as a case study to analyze the phosphorus speciation and distribution of overlying water and sediments in the hyporheic zone, and the phosphorus release process of sediments under the coupling of multiple factors. The results showed that the sediment acted as a phosphorus ' sink ' to accept the input of exogenous industrial and agricultural production. Microorganisms could produce complexes through their own metabolism, related enzyme expression, and sulfur reduction process to promote the transformation of phosphorus in sediments to soluble forms. The direct effect of phytoplankton on promoting phosphorus release from sediments is obvious. Water quality and sediment can indirectly promote the release of biological available phosphorus by promoting the proliferation of phytoplankton. As the demand for available phosphorus by phytoplankton increases, phosphorus-related bacterial communities show a stronger ability to decompose phosphorus. The functional genes of microorganisms involved in the phosphorous cycle are also coupled in this system, thus forming a sediment-water quality-biological activity coupling system that plays an important role in promoting sediment phosphorus release. The results of this study provide a theoretical reference for further research on the transformation and circulation of nutrient elements in the complex environment of rivers.

Marine phytoplankton impose strong selective pressures on in vitro microbiome assembly, but drift is the dominant process

Phytoplankton are known ecosystem engineers that modulate ocean community assembly processes, but the universality and extent of their microbiome control remains unclear. We used in vitro incubations and 16S ribosomal RNA gene amplicon sequencing to test the influence of Southern and South Pacific oceans dominant phytoplankton on assembly processes and community successions in response to phytoplankton blooms. Phytoplankton grown with reduced-diversity cultures or supplemented with exogenously added microbiomes showed reduced diversity, suggesting environmental filtering. Community profiles were distinct under all culture conditions, further confirming strong selection for specific microbiomes based on phytoplankton. Analysis of core, abundant, and rare organisms in each culture condition showed a conserved response in which core organisms were enriched under conditions of exogenously added phytoplankton. Progression through phytoplankton growth phases selected first for rare and abundant organisms, with increased selection for core members during the exponential phase and relaxing of selection during the death phase, as seen throughout incubations for microbiome-only controls. Surprisingly, selection process quantification identified drift as the dominant process across all conditions and growth phases, with homogenous selection and dispersal limitation accounting for the remainder. Altogether, using Southern Ocean-derived model organisms we confirmed the role phytoplankton play in community assembly but also demonstrated that stochastic processes still predominately drive community selection.

Biotransformation characteristics of urate-lowering probiotic fermented apple juice and potential regulatory mechanisms for ameliorating hyperuricemia via mediating gut microbiota and metabolic pathways

Hyperuricemia has evolved into a global public health concern, and applying probiotics fermented apple juice holds promise for alleviating this condition. This study aimed to investigate the biotransformation and metabolic features of urate-lowering probiotics sequentially fermented dealcoholized apple juice (PSFA), and assess its ameliorative effects and potential mechanisms on hyperuricemia mice. Results showed that CICC 6074 and 20,292 possessed excellent purine, nucleotide and nucleoside degradation and acid and bile salt resistance; sequential fermentation decreased the fructose in apple juice, and viable counts reached 3.76 × 108 CFU/mL. Histopathological analysis showed that PSFA ameliorated kidney damage in hyperuricemia mice. Furthermore, PSFA significantly reduced Urea, Creatinine and Uric acid levels in hyperuricemia mice; and inhibited xanthine oxidase activity and the expression of pro-inflammatory factors. Importantly, PSFA reversed gut microbiota dysbiosis and raised the abundance of beneficial bacteria (Lactobacillush, Faecalibaculum and Lachnospiraceae_NK4A136_group). KEGG and COG functional prediction results revealed that the potential mechanism of PSFA to ameliorate hyperuricemia may be lipid metabolism and glycolysis pathways.

Soil properties drive nitrous oxide accumulation patterns by shaping denitrifying bacteriomes

In agroecosystems, nitrous oxide (N₂O) emissions are influenced by both microbiome composition and soil properties, yet the relative importance of these factors in determining differential N₂O emissions remains unclear. This study investigates the impacts of these factors on N₂O emissions using two primary agricultural soils from northern China: fluvo-aquic soil (FS) from the North China Plain and black soil (BS) from Northeast China, which exhibit significant differences in physicochemical properties. In non-sterilized controls (NSC), we observed distinct denitrifying bacterial phenotypes between FS and BS, with BS exhibiting significantly higher N₂O emissions. Cross-inoculation experiments were conducted by introducing extracted microbiomes into sterile recipient soils of both types to disentangle the relative contributions of soil properties and microbiomes on N₂O emission potential. The results showed recipient-soil-dependent gas kinetics, with significantly higher N₂O/(N₂O + N₂) ratios in BS compared to FS, regardless of the inoculum type. Metagenomic analysis further revealed significant shifts in denitrification genes and microbial diversity of the inoculated bacteriomes influenced by the recipient soil. The higher ratios of nirS/nosZ in FS and nirK/nosZ in BS indicated that the recipient soil dictates the formation of different denitrifying guilds. Specifically, the BS environment fosters nirK-based denitrifiers like Rhodanobacter, contributing to higher N₂O accumulation, while FS supports a diverse array of denitrifiers, including Pseudomonas and Stutzerimonas, associated with complete denitrification and lower N₂O emissions. This study underscores the critical role of soil properties in shaping microbial community dynamics and greenhouse gas emissions. These findings highlight the importance of considering soil physicochemical properties in managing agricultural practices to mitigate N₂O emissions.

Soil-sediment connectivity through Bayesian source tracking in an urban naturalised waterway via microbial and isotopic markers

Riverine sediments are important habitats for microbial activity in naturalised waterways to provide potential ecosystem services that improve stormwater quality. Yet, little is known about the sources of these sediment microbes, and the factors shaping them. This study investigated the dominant source of sediments in a tropical naturalised urban waterway, using two Bayesian methods for microbial and isotopic 13C/15N markers concurrently. Additionally, key factors shaping microbial communities from the surrounding landscape were evaluated. A comprehensive two-year field survey identified source land covers of interest based on topology and soil context. Among these land covers, riverbanks were the dominant source of sediments contribution for both edaphic and microbial components. The physico-chemical environment explains most of the variation in sediment communities compared to inter-location distances and microbial source contribution. As microbes provide ecosystem services important for rewilding waterways, management strategies that establish diverse sediment microbial communities are encouraged. Since riverbanks play a disproportionately important role in material contribution to sediment beds, management practices aimed at controlling soil erosion from riverbanks can improve overall functioning of waterway systems.

Perturbations to common gardens of anaerobic co-digesters reveal relationships between functional resilience and microbial community composition

We report the relationship between enrichment of adapted populations and enhancement of community functional resilience in methanogenic bioreactors. Although previous studies have shown the positive effects of acclimation, this work directly investigated the relationships between microbiome dynamics and performance of anaerobic co-digesting reactors in response to different levels of an environmental perturbation (loading of grease interceptor waste [GIW]). Using the methanogenic microbiome from a full-scale digester, we developed eight sets of microbial communities in triplicate using different feed sources. These substrate-specific microbiomes were then exposed to three independent disturbance events of low-, mid- and high-GIW loading rates. This approach allowed us to directly attribute differences in community responses to differences in community composition. Despite identical inocula, environment (digester operation, substrate loading rate, and feeding patterns) and general whole-community function (methane production and effluent quality) during the cultivation period, different substrates led to different microbial community assemblies. Lipid pre-acclimation led to enrichment of a pool of specialized populations, along with thriving of sub-dominant communities. The enrichment of these populations improved functional resilience and process performance when exposed to a low level of lipid-rich perturbation compared with less-acclimated communities. At higher levels of perturbation, the communities were not able to recover methanogenesis, indicating a loading limit to the resilience response. This study extends our current understanding of environmental perturbations, feed-specific adaptation, and functional resilience in methanogenic bioreactors.IMPORTANCEThis study demonstrates, for the first time for GIW co-digestion, how applying similar perturbations to different microbial communities was used to directly identify the causal relationships between microbial community, function, and environment in triplicate anaerobic microbiomes. We evaluated the impact of feed-specific adaptation on methanogenic microbiomes and demonstrated how microbiomes can be influenced to improve their functional (methanogenic) resilience to GIW inhibition. These findings demonstrate how an ecological framework can help improve a biological engineering application, and more specifically, increase the potential of anaerobic co-digestion for converting wastes to energy.

Limiting Resources Define the Global Pattern of Soil Microbial Carbon Use Efficiency

Microbial carbon (C) use efficiency (CUE) delineates the proportion of organic C used by microorganisms for anabolism and ultimately influences the amount of C sequestered in soils. However, the key factors controlling CUE remain enigmatic, leading to considerable uncertainty in understanding soil C retention and predicting its responses to global change factors. Here, we investigate the global patterns of CUE estimate by stoichiometric modeling in surface soils of natural ecosystems, and examine its associations with temperature, precipitation, plant-derived C and soil nutrient availability. We found that CUE is determined by the most limiting resource among these four basic environmental resources within specific climate zones (i.e., tropical, temperate, arid, and cold zones). Higher CUE is common in arid and cold zones and corresponds to limitations in temperature, water, and plant-derived C input, while lower CUE is observed in tropical and temperate zones with widespread limitation of nutrients (e.g., nitrogen or phosphorus) in soil. The contrasting resource limitations among climate zones led to an apparent increase in CUE with increasing latitude. The resource-specific dependence of CUE implies that soils in high latitudes with arid and cold environments may retain less organic C in the future, as warming and increased precipitation can reduce CUE. In contrast, oligotrophic soils in low latitudes may increase organic C retention, as CUE could be increased with concurrent anthropogenic nutrient inputs. The findings underscore the importance of resource limitations for CUE and suggest asymmetric responses of organic C retention in soils across latitudes to global change factors.

Climate-driven succession in marine microbiome biodiversity and biogeochemical function

Seasonal and El Niño-Southern Oscillation (ENSO) warming result in similar ocean changes as predicted with climate change. Climate-driven environmental cycles have strong impacts on microbiome diversity, but impacts on microbiome function are poorly understood. We quantified changes in microbial genomic diversity and functioning over 11 years covering seasonal and ENSO cycles at a coastal site in the southern California Current. We observed seasonal oscillations between large genome lineages during cold, nutrient rich conditions in winter and spring versus small genome lineages, including Prochlorococcus and Pelagibacter , in summer and fall. Parallel interannual changes separated communities depending on ENSO condition. Biodiversity shifts translated into clear oscillations in microbiome functional potential. Ocean warming induced an ecosystem with less iron but more macronutrient stress genes, depressed organic carbon degradation potential and biomass, and elevated carbon-to-nutrient biomass ratios. The consistent microbial response observed across time-scales points towards large climate-driven changes in marine ecosystems and biogeochemical cycles.

Global patterns in the growth potential of soil bacterial communities

Despite the growing catalogue of studies detailing the taxonomic and functional composition of soil bacterial communities, the life history traits of those communities remain largely unknown. This study analyzes a global dataset of soil metagenomes to explore environmental drivers of growth potential, a fundamental aspect of bacterial life history. We find that growth potential, estimated from codon usage statistics, was highest in forested biomes and lowest in arid latitudes. This indicates that bacterial productivity generally reflects ecosystem productivity globally. Accordingly, the strongest environmental predictors of growth potential were productivity indicators, such as distance to the equator, and soil properties that vary along productivity gradients, such as pH and carbon to nitrogen ratios. We also observe that growth potential was negatively correlated with the relative abundances of genes involved in carbohydrate metabolism, demonstrating tradeoffs between growth and resource acquisition in soil bacteria. Overall, we identify macroecological patterns in bacterial growth potential and link growth rates to soil carbon cycling.

Effects of exogenous copper on microbial metabolic function and carbon use efficiency of Panax notoginseng planting soil

Soil copper (Cu) pollution is a serious environmental risk in the Panax notoginseng planting area. However, the effect of Cu on soil microbial metabolism and nutrient cycling in this area remains unknown. Therefore, Biolog ECO-plate and enzyme stoichiometry methods were utilized in this study to investigate the impact of exogenous Cu (control: 0 mg·kg-1; Cu100: 100 mg·kg-1; Cu400: 400 mg·kg-1; and Cu600: 600 mg·kg-1) on the metabolic function of soil microbial and nutrient limitation in the P. notoginseng soil. The results indicated that Cu100 significantly increased soil organic carbon (SOC), total phosphorus (TP), soil C:N, microbial biomass carbon (MBC), and microbial biomass nitrogen (MBN) 9.89%, 15.65%, 17.91%, 61.87%, and 90.56% higher than the control, respectively. Moreover, the carbon source utilization ratio of carbohydrates, amino acids, and amphiphilic compounds of Cu100 also increased by 7.16%, 25.47%, and 84.68%, respectively, compared with the control. The activities of β-1,4-glucosidase, cellobiohyrolase, leucine amino peptidase, β-1,4-N-acetylglucosaminidase, and phosphatase significantly decreased with increasing Cu concentration. Soil enzyme stoichiometry showed that all treatments were limited by nitrogen (vector angle < 45°; 19.045-22.081). Cu600 led to the lowest carbon limitation (1.798) and highest carbon use efficiency (CUE:0.267). The PLS-SEM model also showed that MBC, MBN, MBP, and microbial diversity positively affected carbon and nitrogen limitation (0.654 and 0.424). Soil carbon, nitrogen, phosphorus, stoichiometric ratio, MBC, MBN, and MBP positively affected CUE (0.527 and 0.589). The microbial diversity index significantly negatively affected CUE (-1.490). Multiple linear stepwise regression analyses showed that CUE was mainly influenced by MBC, AP, C:P, and LAP. Thus, P. notoginseng soil can benefit soil microbial carbon and nitrogen limitations at low Cu concentrations. Clarifying the metabolic activity and nutritional status of microorganisms under Cu stress can provide some theoretical basis for realizing China's comprehensive and effective management and control policies for environmental risks from metals by 2035.

Genomic fingerprints of the world's soil ecosystems

Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes-more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.IMPORTANCEWe address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1,512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. Our work reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step toward comprehending the intricate world of soil microorganisms and its role in the global climate.

Towards establishing a fungal economics spectrum in soil saprobic fungi

Trait-based frameworks are promising tools to understand the functional consequences of community shifts in response to environmental change. The applicability of these tools to soil microbes is limited by a lack of functional trait data and a focus on categorical traits. To address this gap for an important group of soil microorganisms, we identify trade-offs underlying a fungal economics spectrum based on a large trait collection in 28 saprobic fungal isolates, derived from a common grassland soil and grown in culture plates. In this dataset, ecologically relevant trait variation is best captured by a three-dimensional fungal economics space. The primary explanatory axis represents a dense-fast continuum, resembling dominant life-history trade-offs in other taxa. A second significant axis reflects mycelial flexibility, and a third one carbon acquisition traits. All three axes correlate with traits involved in soil carbon cycling. Since stress tolerance and fundamental niche gradients are primarily related to the dense-fast continuum, traits of the 2nd (carbon-use efficiency) and especially the 3rd (decomposition) orthogonal axes are independent of tested environmental stressors. These findings suggest a fungal economics space which can now be tested at broader scales.

Decoding populations in the ocean microbiome

Understanding the characteristics and structure of populations is fundamental to comprehending ecosystem processes and evolutionary adaptations. While the study of animal and plant populations has spanned a few centuries, microbial populations have been under scientific scrutiny for a considerably shorter period. In the ocean, analyzing the genetic composition of microbial populations and their adaptations to multiple niches can yield important insights into ecosystem function and the microbiome's response to global change. However, microbial populations have remained elusive to the scientific community due to the challenges associated with isolating microorganisms in the laboratory. Today, advancements in large-scale metagenomics and metatranscriptomics facilitate the investigation of populations from many uncultured microbial species directly from their habitats. The knowledge acquired thus far reveals substantial genetic diversity among various microbial species, showcasing distinct patterns of population differentiation and adaptations, and highlighting the significant role of selection in structuring populations. In the coming years, population genomics is expected to significantly increase our understanding of the architecture and functioning of the ocean microbiome, providing insights into its vulnerability or resilience in the face of ongoing global change. Video Abstract.

Functional antagonism and insights into the biosynthetic potential of human gut-derived microbes

The specialised small molecules encoded by commensal microbes mediate distinct functional interactions. However, there is a landscape of antagonistic interactions mediated by specialised strains and their small molecules. Herein, the antagonistic landscape within a collection of 330 human gut-derived commensal microbial strains was elucidated to evaluate antimicrobial interactions as a defensive contributor, and gain new insights into structure-related functions. The potential antagonistic gut-derived strains displayed strain-specific selective inhibition. This is in contrast to common antimicrobial drugs, which typically wipe out a broad range of species and are usually found in environmental microbes. Genome sequencing of representative gut strains revealed the presence of significant biosynthetic gene clusters (BGCs) encoding compound families that contribute to antagonistic activities, and are important in host defence and maintaining gut homeostasis. Subsets of these BGCs were abundant in metagenomic sequencing data from healthy individuals. Furthermore, the cell culture secretome of these strains revealed potential biomarkers linked to hallmark pathways. These microorganisms have biosynthetic novelty and are a source of biologically significant natural products. Such natural products are essential in the development of new antimicrobial agents to reduce the usage of broad-spectrum antibiotics and combat antimicrobial resistance.

Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model

Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.

Bacterial population-level trade-offs between drought tolerance and resource acquisition traits impact decomposition

Microbes drive fundamental ecosystem processes, such as decomposition. Environmental stressors are known to affect microbes, their fitness, and the ecosystem functions that they perform; yet, understanding the causal mechanisms behind this influence has been difficult. We used leaf litter on soil surface as a model in situ system to assess changes in bacterial genomic traits and decomposition rates for 18 months with drought as a stressor. We hypothesized that genome-scale trade-offs due to investment in stress tolerance traits under drought reduce the capacity for bacterial populations to carry out decomposition, and that these population-level trade-offs scale up to impact emergent community traits, thereby reducing decomposition rates. We observed drought tolerance mechanisms that were heightened in bacterial populations under drought, identified as higher gene copy numbers in metagenome-assembled genomes. A subset of populations under drought had reduced carbohydrate-active enzyme genes that suggested-as a trade-off-a decline in decomposition capabilities. These trade-offs were driven by community succession and taxonomic shifts as distinct patterns appeared in populations. We show that trait-trade-offs in bacterial populations under drought could scale up to reduce overall decomposition capabilities and litter decay rates. Using a trait-based approach to assess the population ecology of soil bacteria, we demonstrate genome-level trade-offs in response to drought with consequences for decomposition rates.

Co-inoculations of bacteria and mycorrhizal fungi often drive additive plant growth responses

Controlled greenhouse studies have shown the numerous ways that soil microbes can impact plant growth and development. However, natural soil communities are highly complex, and plants interact with many bacterial and fungal taxa simultaneously. Due to logistical challenges associated with manipulating more complex microbiome communities, how microbial communities impact emergent patterns of plant growth therefore remains poorly understood. For instance, do the interactions between bacteria and fungi generally yield additive (i.e. sum of their parts) or nonadditive, higher order plant growth responses? Without this information, our ability to accurately predict plant responses to microbial inoculants is weakened. To address these issues, we conducted a meta-analysis to determine the type (additive or higher-order, nonadditive interactions), frequency, direction (positive or negative), and strength that bacteria and mycorrhizal fungi (arbuscular and ectomycorrhizal) have on six phenotypic plant growth responses. Our results demonstrate that co-inoculations of bacteria and mycorrhizal fungi tend to have positive additive effects on many commonly reported plant responses. However, ectomycorrhizal plant shoot height responds positively and nonadditively to co-inoculations of bacteria and ectomycorrhizal fungi, and the strength of additive effects also differs between mycorrhizae type. These findings suggest that inferences from greenhouse studies likely scale to more complex field settings and that inoculating plants with diverse, beneficial microbes is a sound strategy to support plant growth.

Response mechanism of sediment endogenous phosphorus release to functional microorganisms and its cyanobacterial growth and disappearance effects

Endogenous phosphorus (P) release from lake sediments is an important factor in the eutrophication of overlying waters, as P is the limiting nutrient salt affecting cyanobacterial growth. Microorganisms are also key to the evolution of cyanobacterial growth and disappearance, as they can influence the release of endogenous P. Meanwhile, endogenous phosphorus can also have an impact on microbial structure. However, there is a lack of studies on the response mechanisms between endogenous P release and microorganisms, as well as the exploration of endogenous P release on the whole cyanobacterial growth and disappearance evolution process. In this study, metagenome sequencing was used to characterize the microbial community structure at different times and to explain the P cycle from the perspective of functional genes. The results showed that the number of sediment microorganisms (genes) gradually increased with the P release capacity, and the outbreak with the strongest P release capacity possessed the most abundant microorganisms (genes). Proteobacteria with P solubilizing functions were consistently the most abundant phylum in all four periods and were positively correlated with P release potential assessment factors EPC0, EPC0F, and NAP. Functional genes affect the P cycle by acting primarily on inorganic P solubilization, organic P mineralization, and P transport. These P-functional genes are mainly found in Proteobacteria, Acidobacteria, Chloroflexi, and Actinobacteria microorganisms. In addition, the P form in the sediments was dominated by IP, with the highest concentration (704.86 mg/kg) occurring during the dormant period. Sediments from this period acted as a strong P "sink", creating a precondition for cyanobacterial recovery and outbreaks to provide a source of P. The results of this study can provide a theoretical basis for controlling endogenous P release at the microscopic level of cyanobacterial growth and disappearance.

Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient

Bacterial gene repertoires reflect adaptive strategies, contribute to ecosystem functioning and are limited by genome size. However, gene functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, we analyse gene functional diversity (by shotgun metagenomics) and taxonomic diversity (by 16S rRNA gene amplicon sequencing) to investigate soil bacterial communities along a natural pH gradient in 12 tropical, subtropical, and temperate forests. We find that bacterial average genome size and gene functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral; as a result, bacterial taxonomic and functional diversity are negatively correlated. The gene repertoire of acid-adapted oligotrophs is enriched in functions of signal transduction, cell motility, secretion system, and degradation of complex compounds, while that of neutral pH-adapted copiotrophs is enriched in functions of energy metabolism and membrane transport. Our results indicate that a mismatch between taxonomic and functional diversity can arise when environmental factors (such as pH) select for adaptive strategies that affect genome size distributions.

Global scale phylogeography of functional traits and microdiversity in Prochlorococcus

Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenome-assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenome-assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype's phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus.

Evaluating the role of bacterial diversity in supporting soil ecosystem functions under anthropogenic stress

Ecosystem functions and services are under threat from anthropogenic global change at a planetary scale. Microorganisms are the dominant drivers of nearly all ecosystem functions and therefore ecosystem-scale responses are dependent on responses of resident microbial communities. However, the specific characteristics of microbial communities that contribute to ecosystem stability under anthropogenic stress are unknown. We evaluated bacterial drivers of ecosystem stability by generating wide experimental gradients of bacterial diversity in soils, applying stress to the soils, and measuring responses of several microbial-mediated ecosystem processes, including C and N cycling rates and soil enzyme activities. Some processes (e.g., C mineralization) exhibited positive correlations with bacterial diversity and losses of diversity resulted in reduced stability of nearly all processes. However, comprehensive evaluation of all potential bacterial drivers of the processes revealed that bacterial α diversity per se was never among the most important predictors of ecosystem functions. Instead, key predictors included total microbial biomass, 16S gene abundance, bacterial ASV membership, and abundances of specific prokaryotic taxa and functional groups (e.g., nitrifying taxa). These results suggest that bacterial α diversity may be a useful indicator of soil ecosystem function and stability, but that other characteristics of bacterial communities are stronger statistical predictors of ecosystem function and better reflect the biological mechanisms by which microbial communities influence ecosystems. Overall, our results provide insight into the role of microorganisms in supporting ecosystem function and stability by identifying specific characteristics of bacterial communities that are critical for understanding and predicting ecosystem responses to global change.

Transfer route and driving forces of antibiotic resistance genes from reclaimed water to groundwater

The infiltration of reclaimed water has created a significant environmental risk due to the spread of antibiotic resistance genes (ARGs) in riparian groundwater. Reclaimed water from wastewater treatment plants (WWTPs) had been identified as a source of both antibiotics and ARGs in groundwater, based on their spatial and temporal distribution. The assembly process of microbial communities in the groundwater of the infiltration zone was more influenced by deterministic processes. Co-occurrence network analysis revealed that Thermotoga, Desulfotomaculum, Methanobacterium, and other such genera were dominant shared genera. These were considered core genera and hosts of ARGs for transport from reclaimed water to groundwater. The most abundant ARG in these shared genera was MacB, enriched in groundwater point G3 and potentially transferred from reclaimed water to groundwater by Acidovorax, Hydrogenophaga, Methylotenera, Dechloromonas, and Nitrospira. During the infiltration process, environmental factors and the tradeoff between energy metabolism and antibiotic defense strategy may have affected ARG transfer. Understanding the transfer route and driving forces of ARGs from reclaimed water to groundwater provided a new perspective for evaluating the spread risk of ARGs in reclaimed water infiltration.

Nutrient and stoichiometry dynamics of decomposing litter in stream ecosystems: A global synthesis

Decomposing organic matter forms a substantial resource base fueling the biogeochemical function and secondary production of most aquatic ecosystems. However, detrital N (nitrogen) and P (phosphorus) dynamics remain relatively unexplored in aquatic relative to terrestrial ecosystems, despite fundamentally linking microbial processes to ecosystem function across broad spatial scales. We synthesized 217 published time series of detrital carbon (C), N, P, and their stoichiometric ratios (C:N, C:P, N:P) from stream ecosystems to analyze the temporal nutrient dynamics of decomposing litter using generalized additive models. Model results indicated that detritus was a net source of N (irrespective of inorganic or organic form) to the environment regardless of initial N content. In contrast, P sink/source dynamics were more strongly influenced by initial P content, where P-poor litters were sinks of nutrients until shifting to net P mineralization after ~40% mass loss. However, large variation surrounded both N and P predictions, suggesting the importance of non-microbial factors such as fragmentation by invertebrates. Detrital C:N ratios converged and became more similar toward the end of decomposition, suggesting predictable microbial functional effects throughout detrital ontogeny. C:P and N:P ratios also converged to some degree, but these model predictions were less robust than for C:N, due in part to the lower number of published detrital C:P time series. Explorations of environmental covariate effects were frequently limited by few coincident covariate measurements across studies, but temperature, N availability, and P tended to accelerate existing ontogenetic patterns in C:N. Our analysis helps unite organic matter decomposition across aquatic-terrestrial boundaries by describing basic patterns of elemental flows catalyzed by decomposition in streams, and points to a research agenda to continue addressing gaps in our knowledge of detrital nutrient dynamics across ecosystems. This article is protected by copyright. All rights reserved.

The reciprocal changes in dominant species with complete metabolic functions explain the decoupling phenomenon of microbial taxonomic and functional composition in a grassland

The decoupling of microbial functional and taxonomic components refers to the phenomenon that a drastic change in microbial taxonomic composition leads to no or only a gentle change in functional composition. Although many studies have identified this phenomenon, the mechanisms underlying it are still unclear. Here we demonstrate, using metagenomics data from a steppe grassland soil under different grazing and phosphorus addition treatments, that there is no “decoupling” in the variation of taxonomic and metabolic functional composition of the microbial community within functional groups at species level. In contrast, the high consistency and complementarity between the abundance and functional gene diversity of two dominant species made metabolic functions unaffected by grazing and phosphorus addition. This complementarity between the two dominant species shapes a bistability pattern that differs from functional redundancy in that only two species cannot form observable redundancy in a large microbial community. In other words, the “monopoly” of metabolic functions by the two most abundant species leads to the disappearance of functional redundancy. Our findings imply that for soil microbial communities, the impact of species identity on metabolic functions is much greater than that of species diversity, and it is more important to monitor the dynamics of key dominant microorganisms for accurately predicting the changes in the metabolic functions of the ecosystems.

Global scale phylogeography of functional traits and microdiversity in Prochlorococcus

Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenomically assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenomically assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype’s phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus .

Response of soil microbial communities and rice yield to nitrogen reduction with green manure application in karst paddy areas

Fertilizer application practices are one of the major challenges facing agroecology. The agrobenefits of combined application of green manure and chemical fertilizers, and the potential of green manure to replace chemical fertilizers are now well documented. However, little is known about the impact of fertilization practices on microbial communities and tice yield. In this study, the diversity of bacterial and fungal communities, symbiotic networks and their relationship with soil function were analyzed in five fertilization treatments (N: 100% nitrogen fertilizer alone; M: green manure alone; MN₆₀: green manure couple with 60% nitrogen fertilizer, MN₈₀: green manure couple with 80% nitrogen fertilizer; and MN₁₀₀: green manure couple with 100% nitrogen fertilizer). First, early rice yield was significantly higher by 12.6% in MN₁₀₀ treatment in 2021 compared with N. Secondly, soil bacterial diversity showed an increasing trend with increasing N fertilizer application after green manure input, however, the opposite was true for fungal diversity. Microbial interaction analysis showed that different fertilizer applications changed soil microbial network complexity and fertilizer-induced changes in soil microbial interactions were closely related to soil environmental changes. Random forest models further predicted the importance of soil environment, microorganisms and rice yield. Overall, nitrogen fertilizer green manure altered rice yield due to its effects on soil environment and microbial communities. In the case of combined green manure and N fertilizer application, bacteria and fungi showed different responses to fertilization method, and the full amount of N fertilizer in combination with green manure reduced the complexity of soil microbial network. In contrast, for more ecologically sensitive karst areas, we recommend fertilization practices with reduced N by 20-40% for rice production. Graphical Abstract.

Development of Candida autochthonous starter for cigar fermentation via dissecting the microbiome

Introduction

The main goal of tobacco fermentation technology is to minimize the alkaloid content while improving flavor substance content.

Methods

This study revealed the microbial community structure and their metabolic functions during cigar leaf fermentation by high-throughput sequencing and correlation analysis, and evaluated the fermentation performance of functional microbes based on in vitro isolation and bioaugmentation fermentation.

Results

The relative abundance of Staphylococcus and Aspergillus increased first but then decreased during the fermentation, and would occupy the dominant position of bacterial and fungal communities, respectively, on the 21st day. Correlation analysis predicted that Aspergillus, Staphylococcus and Filobasidium could contribute to the formation of saccharide compounds, Bacillus might have degradation effects on nitrogenous substances. In particular, Candida, as a co-occurring taxa and biomarker in the later stage of fermentation, could not only degrade nitrogenous substrates and synthesize flavor substances, but also contribute to maintaining the stability of microbial community. Moreover, based on in vitro isolation and bioaugmentation inoculation, it was found that Candida parapsilosis and Candida metapsilosis could significantly reduce the alkaloids content and increase the content of flavor components in tobacco leaves.

Discussion

This study found and validated the critical role of Candida in the fermentation of cigar tobacco leaves through high-throughput sequencing and bioaugmentation inoculation, which would help guide the development of microbial starters and directional regulation of cigar tobacco quality.

Identification and validation of core microbes associated with key aroma formation in fermented pepper paste (Capsicum annuumL.)

Fermented peppers are usually obtained by the spontaneous fermentation of microorganisms attached to fresh peppers, and the variable microbial composition would lead to inconsistencies in flavor between batches. To demonstrate the roles of microorganisms in flavor formation, the core microbes closely associated with the key aroma compounds of fermented pepper paste were screened and validated in this study. Lactobacillus was the dominant bacterial genus in fermented pepper paste, whereas the main fungal genera were Alternaria and Kazachstania. Nine strains of the genera Lactobacillus, Weissella, Bacillus, Zygosaccharomyces, Kazachstania, Debaryomyces, and Pichia were isolated from fermented pepper paste. Eleven key aroma compounds were identified using gas chromatography combined with olfactometry and relative odor activity values. Correlation analysis showed that Zygosaccharomyces and Kazachstania were positively correlated with the majority of the key aroma compounds, whereas Lactobacillus was negatively correlated with them. Thus, Zygosaccharomyces and Kazachstania were identified as core genera associated with the key odorants. Finally, Zygosaccharomyces bisporus, Kazachstania humilis, and Lactiplantibacillus plantarum were used as starter cultures for fermented peppers, confirming that Z. bisporus and K. humilis were more beneficial for the key aroma compounds (e.g., acetate, linalool, and phenyl ethanol) rather than L. plantarum. This study contributed to understanding the flavor formation mechanism and provided references for the quality control of food fermentation.

Bacterioplankton dispersal and biogeochemical function across Alaskan Arctic catchments

In Arctic catchments, bacterioplankton are dispersed through soils and streams, both of which freeze and thaw/flow in phase, seasonally. To characterize this dispersal and its potential impact on biogeochemistry, we collected bacterioplankton and measured stream physicochemistry during snowmelt and after vegetation senescence across multiple stream orders in alpine, tundra, and tundra-dominated-by-lakes catchments. In all catchments, differences in community composition were associated with seasonal thaw, then attachment status (i.e. free floating or sediment associated), and then stream order. Bacterioplankton taxonomic diversity and richness were elevated in sediment-associated fractions and in higher-order reaches during snowmelt. Families Chthonomonadaceae, Pyrinomonadaceae, and Xiphinematobacteraceae were abundantly different across seasons, while Flavobacteriaceae and Microscillaceae were abundantly different between free-floating and sediment-associated fractions. Physicochemical data suggested there was high iron (Fe⁺ ) production (alpine catchment); Fe⁺ production and chloride (Cl^- ) removal (tundra catchment); and phosphorus (SRP) removal and ammonium (NH₄ ⁺ ) production (lake catchment). In tundra landscapes, these 'hot spots' of Fe⁺ production and Cl^- removal accompanied shifts in species richness, while SRP promoted the antecedent community. Our findings suggest that freshet increases bacterial dispersal from headwater catchments to receiving catchments, where bacterioplankton-mineral relations stabilized communities in free-flowing reaches, but bacterioplankton-nutrient relations stabilized those punctuated by lakes.

Multiple anthropogenic pressures eliminate the effects of soil microbial diversity on ecosystem functions in experimental microcosms

Biodiversity is crucial for the provision of ecosystem functions. However, ecosystems are now exposed to a rapidly growing number of anthropogenic pressures, and it remains unknown whether biodiversity can still promote ecosystem functions under multifaceted pressures. Here we investigated the effects of soil microbial diversity on soil functions and properties when faced with an increasing number of simultaneous global change factors in experimental microcosms. Higher soil microbial diversity had a positive effect on soil functions and properties when no or few (i.e., 1–4) global change factors were applied, but this positive effect was eliminated by the co-occurrence of numerous global change factors. This was attributable to the reduction of soil fungal abundance and the relative abundance of an ecological cluster of coexisting soil bacterial and fungal taxa. Our study indicates that reducing the number of anthropogenic pressures should be a goal in ecosystem management, in addition to biodiversity conservation.

It is unclear whether the positive effects of biodiversity on ecosystem functioning are maintained under multifaceted anthropogenic disturbance. In this experiment, the authors show that multiple simultaneous stressors can negate the positive effect of microbial diversity on soil functions.

Causal discovery for the microbiome

Measurement and manipulation of the microbiome is generally considered to have great potential for understanding the causes of complex diseases in humans, developing new therapies, and finding preventive measures. Many studies have found significant associations between the microbiome and various diseases; however, Koch's classical postulates remind us about the importance of causative reasoning when considering the relationship between microbes and a disease manifestation. Although causal discovery in observational microbiome data faces many challenges, methodological advances in causal structure learning have improved the potential of data-driven prediction of causal effects in large-scale biological systems. In this Personal View, we show the capability of existing methods for inferring causal effects from metagenomic data, and we highlight ways in which the introduction of causal structures that are more flexible than existing structures offers new opportunities for causal reasoning. Our observations suggest that microbiome research can further benefit from tools developed in the past 5 years in causal discovery and learn from their applications elsewhere.

Short-Term Vegetation Restoration Enhances the Complexity of Soil Fungal Network and Decreased the Complexity of Bacterial Network

Different vegetation restoration methods may affect the soil’s physicochemical properties and microbial communities. However, it is not known how the microbial network’s complexity of the bacterial and fungal communities respond to short-term vegetation restoration. We conducted a short-term ecological restoration experiment to reveal the response of the soil’s microbial community and microbial network’s stability to initial vegetation restoration during the restoration of the degraded grassland ecosystem. The two restoration methods (sowing alfalfa (Medicago sativa, AF) and smooth brome (Bromus inermis, SB)) had no significant effect on the alpha diversity of the fungal community, but the SB significantly increased the alpha diversity of the soil surface bacterial community (p < 0.01). The results of NMDS showed that the soil’s fungal and bacterial communities were altered by a short-term vegetation restoration, and they showed that the available phosphorus (AP), available potassium (AK), and nitrate nitrogen (nitrate-N) were closely related to changes in bacterial and fungal communities. Moreover, a short-term vegetation restoration significantly increased the complexity and stability of fungi ecological networks, but the opposite was the case with the bacteria. Our findings confirm that ecological restoration by sowing may be favorable to the amelioration of soil fungi complexity and stability in the short-term. Such findings may have important implications for soil microbial processes in vegetation recovery.

Microbiome assembly in thawing permafrost and its feedbacks to climate

The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost-climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post-thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw-mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well-suited to thrive in changing environmental conditions. We predict that on a short timescale and following high-disturbance thaw (e.g., thermokarst), stochasticity dominates post-thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower-intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post-thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change.

Developing Indicators of Nutrient Pollution in Streams Using 16S rRNA Gene Metabarcoding of Periphyton-Associated Bacteria

Indicators based on nutrient-biota relationships in streams can inform water quality restoration and protection programs. Bacterial assemblages could be particularly useful indicators of nutrient effects because they are species-rich, important contributors to ecosystem processes in streams, and responsive to rapidly changing conditions. Here, we sampled 25 streams weekly (12-14 times each) and used 16S rRNA gene metabarcoding of periphyton-associated bacteria to quantify the effects of total phosphorus (TP) and total nitrogen (TN). Threshold indicator taxa analysis identified assemblage-level changes and amplicon sequence variants (ASVs) that increased or decreased with increasing TP and TN concentrations (i.e., low P, high P, low N, and high N ASVs). Boosted regression trees confirmed that relative abundances of gene sequence reads for these four indicator groups were associated with nutrient concentrations. Gradient forest analysis complemented these results by using multiple predictors and random forest models for each ASV to identify portions of TP and TN gradients at which the greatest changes in assemblage structure occurred. Synthesized statistical results showed bacterial assemblage structure began changing at 24 μg TP/L with the greatest changes occurring from 110 to 195 μg/L. Changes in the bacterial assemblages associated with TN gradually occurred from 275 to 855 μg/L. Taxonomic and phylogenetic analyses showed that low nutrient ASVs were commonly Firmicutes, Verrucomicrobiota, Flavobacteriales, and Caulobacterales, Pseudomonadales, and Rhodobacterales of Proteobacteria, whereas other groups, such as Chitinophagales of Bacteroidota, and Burkholderiales, Rhizobiales, Sphingomonadales, and Steroidobacterales of Proteobacteria comprised the high nutrient ASVs. Overall, the responses of bacterial ASV indicators in this study highlight the utility of metabarcoding periphyton-associated bacteria for quantifying biotic responses to nutrient inputs in streams.

Characterizing temporal variability in streams supports nutrient indicator development using diatom and bacterial DNA metabarcoding

Interest in developing periphytic diatom and bacterial indicators of nutrient effects continues to grow in support of the assessment and management of stream ecosystems and their watersheds. However, temporal variability could confound relationships between indicators and nutrients, subsequently affecting assessment outcomes. To document how temporal variability affects measures of diatom and bacterial assemblages obtained from DNA metabarcoding, we conducted weekly periphyton and nutrient sampling from July to October 2016 in 25 streams in a 1293 km2 mixed land use watershed. Measures of both diatom and bacterial assemblages were strongly associated with the percent agriculture in upstream watersheds and total phosphorus (TP) and total nitrogen (TN) concentrations. Temporal variability in TP and TN concentrations increased with greater amounts of agriculture in watersheds, but overall diatom and bacterial assemblage variability within sites-measured as mean distance among samples to corresponding site centroids in ordination space-remained consistent. This consistency was due in part to offsets between decreasing variability in relative abundances of taxa typical of low nutrient conditions and increasing variability in those typical of high nutrient conditions as mean concentrations of TP and TN increased within sites. Weekly low and high nutrient diatom and bacterial metrics were more strongly correlated with site mean nutrient concentrations over the sampling period than with same day measurements and more strongly correlated with TP than with TN. Correlations with TP concentrations were consistently strong throughout the study except briefly following two major precipitation events. Following these events, biotic relationships with TP reestablished within one to three weeks. Collectively, these results can strengthen interpretations of survey results and inform monitoring strategies and decision making. These findings have direct applications for improving the use of diatoms and bacteria, and the use of DNA metabarcoding, in monitoring programs and stream site assessments.

Microbial Remediation: A Promising Tool for Reclamation of Contaminated Sites with Special Emphasis on Heavy Metal and Pesticide Pollution: A Review

Heavy metal and pesticide pollution have become an inevitable part of the modern industrialized environment that find their way into all ecosystems. Because of their persistent nature, recalcitrance, high toxicity and biological enrichment, metal and pesticide pollution has threatened the stability of the environment as well as the health of living beings. Due to the environmental persistence of heavy metals and pesticides, they get accumulated in the environs and consequently lead to food chain contamination. Therefore, remediation of heavy metals and pesticide contaminations needs to be addressed as a high priority. Various physico-chemical approaches have been employed for this purpose, but they have significant drawbacks such as high expenses, high labor, alteration in soil properties, disruption of native soil microflora and generation of toxic by-products. Researchers worldwide are focusing on bioremediation strategies to overcome this multifaceted problem, i.e., the removal, immobilization and detoxification of pesticides and heavy metals, in the most efficient and cost-effective ways. For a period of millions of evolutionary years, microorganisms have become resistant to intoxicants and have developed the capability to remediate heavy metal ions and pesticides, and as a result, they have helped in the restoration of the natural state of degraded environs with long term environmental benefits. Keeping in view the environmental and health concerns imposed by heavy metals and pesticides in our society, we aimed to present a generalized picture of the bioremediation capacity of microorganisms. We explore the use of bacteria, fungi, algae and genetically engineered microbes for the remediation of both metals and pesticides. This review summarizes the major detoxification pathways and bioremediation technologies; in addition to that, a brief account is given of molecular approaches such as systemic biology, gene editing and omics that have enhanced the bioremediation process and widened its microbiological techniques toward the remediation of heavy metals and pesticides.

Bulk and Spatially Resolved Extracellular Metabolome of Free-Living Nitrogen Fixation

Soil nitrogen (N) transformations constrain terrestrial net primary productivity and are driven by the activity of soil microorganisms. Free-living N fixation (FLNF) is an important soil N transformation and key N input to terrestrial systems, but the forms of N contributed to soil by FLNF are poorly understood. To address this knowledge gap, a focus on microorganisms and microbial scale processes is needed that links N-fixing bacteria and their contributed N sources to FLNF process rates. However, studying the activity of soil microorganisms in situ poses inherent challenges, including differences in sampling scale between microorganism and process rates, which can be addressed with culture-based studies and an emphasis on microbial-scale measurements. Culture conditions can differ significantly from soil conditions, so it also important that such studies include multiple culture conditions like liquid and solid media as proxies for soil environments like soil pore water and soil aggregate surfaces. Here we characterized extracellular N-containing metabolites produced by two common, diazotrophic soil bacteria in liquid and solid media, with or without N, across two sampling scales (bulk via GC-MS and spatially resolved via MALDI mass spec imaging). We found extracellular production of inorganic and organic N during FLNF, indicating terrestrial N contributions from FLNF occur in multiple forms not only as ammonium as previously thought. Extracellular metabolite profiles differed between liquid and solid media supporting previous work indicating environmental structure influences microbial function. Metabolite profiles also differed between sampling scales underscoring the need to quantify microbial scale conditions to accurately interpret microbial function.

IMPORTANCE Free-living nitrogen-fixing bacteria contribute significantly to terrestrial nitrogen availability; however, the forms of nitrogen contributed by this process are poorly understood. This is in part because of inherent challenges to studying soil microorganisms in situ, such as vast differences in scale between microorganism and ecosystem and complexities of the soil system (e.g., opacity, chemical complexity). Thus, upscaling important ecosystem processes driven by soil microorganisms, like free-living nitrogen fixation, requires microbial-scale measurements in controlled systems. Our work generated bulk and spatially resolved measurements of nitrogen released during free-living nitrogen fixation under two contrasting growth conditions analogous to soil pores and aggregates. This work allowed us to determine that diverse forms of nitrogen are likely contributed to terrestrial systems by free-living nitrogen bacteria. We also demonstrated that microbial habitat (e.g., liquid versus solid media) alters microbial activity and that measurement of microbial activity is altered by sampling scale (e.g., bulk versus spatially resolved) highlighting the critical importance of quantifying microbial-scale processes to upscaling of ecosystem function.

Functional Redundancy in Soil Microbial Community Based on Metagenomics Across the Globe

Understanding the contribution of soil microbial communities to ecosystem processes is critical for predicting terrestrial ecosystem feedbacks under changing climate. Our current understanding lacks a consistent strategy to formulate the linkage between microbial systems and ecosystem processes due to the presumption of functional redundancy in soil microbes. Here we present a global soil microbial metagenomic analysis to generalize patterns of microbial taxonomic compositions and functional potentials across climate and geochemical gradient. Our analyses show that soil microbial taxonomic composition varies widely in response to climate and soil physicochemical gradients, while microbial functional attributes based on metagenomic gene abundances are redundant. Among 17 climate zones, microbial taxonomic compositions were more distinct than functional potentials, as climate and edaphic properties showed more significant influence on microbial taxonomic compositions than on functional potentials. Microbial taxonomies formed a larger and more complex co-occurrence network with more module structures than functional potentials. Functional network was strongly inter-connected among different categories, whereas taxonomic network was more positively interactive in the same taxonomic groups. This study provides strong evidence to support the hypothesis of functional redundancy in soil microbes, as microbial taxonomic compositions vary to a larger extent than functional potentials based on metagenomic gene abundances in terrestrial ecosystems across the globe.

Forest tree growth is linked to mycorrhizal fungal composition and function across Europe

Most trees form symbioses with ectomycorrhizal fungi (EMF) which influence access to growth-limiting soil resources. Mesocosm experiments repeatedly show that EMF species differentially affect plant development, yet whether these effects ripple up to influence the growth of entire forests remains unknown. Here we tested the effects of EMF composition and functional genes relative to variation in well-known drivers of tree growth by combining paired molecular EMF surveys with high-resolution forest inventory data across 15 European countries. We show that EMF composition was linked to a three-fold difference in tree growth rate even when controlling for the primary abiotic drivers of tree growth. Fast tree growth was associated with EMF communities harboring high inorganic but low organic nitrogen acquisition gene proportions and EMF which form contact versus medium-distance fringe exploration types. These findings suggest that EMF composition is a strong bio-indicator of underlying drivers of tree growth and/or that variation of forest EMF communities causes differences in tree growth. While it may be too early to assign causality or directionality, our study is one of the first to link fine-scale variation within a key component of the forest microbiome to ecosystem functioning at a continental scale.

Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics

The dynamics of microbial processes are difficult to study in natural soil, owing to the small spatial scales on which microorganisms operate and to the opacity and chemical complexity of the soil habitat. To circumvent these challenges, we have created a 3D-bioprinted habitat that mimics aspects of natural soil aggregates while providing a chemically defined and translucent alternative culturing method for soil microorganisms. Our Synthetic Soil Aggregates (SSAs) retain the porosity, permeability, and patchy resource distribution of natural soil aggregates—parameters that are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution genomics, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a model co-culture microbial community and find that it is significantly different from the spatial organization of the same community in liquid culture, indicating a potential for SSAs to reproduce naturally occurring emergent community phenotypes. The SSAs have the potential as a tool to help researchers quantify microbial scale processes in situ and achieve high-resolution data from the interplay between environmental properties and microbial ecology.

Microbial adaptation and impact into the pesticide's degradation

The imprudent use of agrochemicals to control agriculture and household pests is unsafe for the environment. Hence, to protect the environment and diversity of living organisms, the degradation of pesticides has received widespread attention. There are different physical, chemical, and biological methods used to remediate pesticides in contaminated sites. Compared to other methods, biological approaches and their associated techniques are more effective, less expensive and eco-friendly. Microbes secrete several enzymes that can attach pesticides, break down organic compounds, and then convert toxic substances into carbon and water. Thus, there is a lack of knowledge regarding the functional genes and genomic potential of microbial species for the removal of emerging pollutants. Here we address the knowledge gaps by highlighting systematic biology and their role in adaptation of microbial species from agricultural soils with a history of pesticide usage and profiling shifts in functional genes and microbial taxa abundance. Moreover, by co-metabolism, the microbial species fulfill their nutritional requirements and perform more efficiently than single microbial-free cells. But in an open environment, free cells of microbes are not much prominent in the degradation process due to environmental conditions, incompatibilities with mechanical equipment and difficulties associated with evenly distributing inoculum through the agroecosystem. This review highlights emerging techniques involving the removal of pesticides in a field-scale environment like immobilization, biobed, biocomposites, biochar, biofilms, and bioreactors. In these techniques, different microbial cells, enzymes, natural fibers, and strains are used for the effective biodegradation of xenobiotic pesticides.

Environmental stress-discriminatory taxa are associated with high C and N cycling functional potentials in dryland grasslands

Increasing environmental stress strongly affects soil microbial communities, but the responses of the microbial assembly and the functional potential of the dominant microbial community in the presence of environmental stress in drylands are still poorly understood. Here, we undertook a broad appraisal of the abundance, diversity, similarity, community assembly, network properties and functions of soil microbiomes in 82 dryland grasslands along environmental gradients. We found that the bacterial and fungal diversity and community similarity showed different sensitivities to environmental stress (decreased mean annual precipitation (MAP) and soil nutrient levels and increased soil pH), and MAP was the most important factor influencing microbial community patterns. In addition, the dominant subcommunity of both bacteria and fungi was more sensitive to environmental stress than the nondominant subcommunity. Although increasing environmental stress decreased microbial phylogenetic clustering, it had no effects on the stochastic and deterministic assembly process balance. Moreover, we identified 101 bacterial and 34 fungal environmental stress-discriminatory taxa that were sensitive to environmental stress, and these bacterial markers showed a high correlation with the abundance of carbon (C) and nitrogen (N) cycling-related genes, whereas the taxa classified as connectors in the network were mainly correlated with C degradation genes. Our study shows that the different responses of bacteria and fungi to environmental stress bring challenges to predicting microbial function, but a relatively small number of taxa play an important role in driving C and N cycling-related functional genes, indicating that identifying an organism's phenotypic characteristics or traits of key taxa may improve our knowledge of the microbial response to ongoing global changes.