Microscopic life from different angles

BackgroundMicrobial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.ResultsThis study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r = 0.5, p = 0.039) between microbial diversity and seed yield.ConclusionThis study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability.BGDCKW7bTctQq4sh1kxH_XVideo

Microbial mat communities consist of dense populations of microorganisms embedded in exopolymers and/or biomineralized solid phases, and are often found in mm-cm thick assemblages, which can be stratified due to environmental gradients such as light, oxygen or sulfide. Microbial mat communities are commonly observed under extreme environmental conditions, deriving energy primarily from light and/or reduced chemicals to drive autotrophic fixation of carbon dioxide. Microbial mat ecosystems are regarded as living analogues of primordial systems on Earth, and they often form perennial structures with conspicuous stratifications of microbial populations that can be studied in situ under stable conditions for many years. Consequently, microbial mat communities are ideal natural laboratories and represent excellent model systems for studying microbial community structure and function, microbial dynamics and interactions, and discovery of new microorganisms with novel metabolic pathways potentially useful in future industrial and/or medical applications. Due to their relative simplicity and organization, microbial mat communities are often excellent testing grounds for new technologies in microbiology including micro-sensor analysis, stable isotope methodology and modern genomics. Integrative studies of microbial mat communities that combine modern biogeochemical and molecular biological methods with traditional microbiology, macro-ecological approaches, and community network modeling will provide new and detailed insights regarding the systems biology of microbial mats and the complex interplay among individual populations and their physicochemical environment. These processes ultimately control the biogeochemical cycling of energy and/or nutrients in microbial systems. Similarities in microbial community function across different types of communities from highly disparate environments may provide a deeper basis for understanding microbial community dynamics and the ecological role of specific microbial populations. Approaches and concepts developed in highly-constrained, relatively stable natural communities may also provide insights useful for studying and understanding more complex microbial communities.

The mining industry in China plays a pivotal role in economic development but also leads to severe environmental issues, particularly heavy metal pollution in soils. Heavy metal pollution significantly impacts soil microbial communities due to its persistence and long-term residual effects. We assessed changes in microbial diversity, community structure, and assembly mechanisms in selenium-impacted soils. This study investigates the impacts of selenium (Se) and other heavy metals on soil microbial communities in selenium-rich mining areas using full-length 16S rRNA gene sequencing. Our results showed that Se and other heavy metal contamination significantly altered microbial community composition, favoring metal-tolerant phyla such as Proteobacteria, Actinobacteriota and Firmicutes, while reducing the abundance of sensitive groups like Acidobacteriota and Chloroflexi. Microbial diversity decreased as Se and other heavy metal concentrations increased. Mantel test analysis revealed that soil total potassium (TK), soil organic carbon, total nitrogen, and several other metals, including zinc, niobium, titanium (Ti), manganese, rubidium, barium, potassium, cobalt, gallium (Ga), Se, chromium (Cr), vanadium, and copper were significantly and positively correlated with microbial community composition across all soil samples. Random forest analysis showed that soil TK and multiple elements [Cr, Ti, nickel (Ni), Ga and Se] were the most important predictors of bacterial diversity, emphasizing the role of multiple elements in shaping microbial communities. Co-occurrence network analysis revealed that Se and other heavy metal contamination reduced network complexity and stability, with high Se-contaminated soils exhibiting fragmented microbial networks. Community assembly was primarily driven by drift in control soils, whereas dispersal limitation became more prominent in Se-contaminated soils due to heavy metal toxicity. These findings highlight the ecological consequences of heavy metal pollution on microbial communities and offer valuable insights for effective soil management and remediation strategies.

Microbial communities (MCs) create complex metabolic networks in natural habitats and respond to environmental changes by shifts in the community structure. Although members of MCs are often not amenable for cultivation in pure culture, it is possible to obtain a greater diversity of species in the laboratory setting when microorganisms are grown as mixed cultures. In order to mimic the environmental conditions, an appropriate growth medium must be applied. Here, we examined the hypothesis that a greater diversity of microorganisms can be sustained under nutrient-limited conditions. Using a 16 S rRNA amplicon metagenomic approach, we explored the structure of a compost-derived MC. During a five-week time course the MC grown in minimal medium with sugarcane bagasse (SCB) as a sole carbon source showed greater diversity and enrichment in lignocellulose-degrading microorganisms. In contrast, a MC grown in nutrient rich medium with addition of SCB had a lower microbial diversity and limited number of lignocellulolytic species. Our approach provides evidence that factors such as nutrient availability has a significant selective pressure on the biodiversity of microorganisms in MCs. Consequently, nutrient-limited medium may displace bacterial generalist species, leading to an enriched source for mining novel enzymes for biotechnology applications.

Soil microorganisms mediate many processes such as nitrification, denitrification, and methanogenesis that regulate ecosystem functioning and also feed back to influence atmospheric chemistry. These processes are of particular interest in freshwater wetland ecosystems where nutrient cycling is highly responsive to fluctuating hydrology and nutrients and soil gas releases may be sensitive to climate warming. In this review we briefly summarize research from process and taxonomic approaches to the study of wetland biogeochemistry and microbial ecology, and highlight areas where further research is needed to increase our mechanistic understanding of wetland system functioning. Research in wetland biogeochemistry has most often been focused on processes (e.g., methanogenesis), and less often on microbial communities or on populations of specific microorganisms of interest. Research on process has focused on controls over, and rates of, denitrification, methanogenesis, and methanotrophy. There has been some work on sulfate and iron transformations and wetland enzyme activities. Work to date indicates an important process level role for hydrology and soil nutrient status. The impact of plant species composition on processes is potentially critical, but is as yet poorly understood. Research on microbial communities in wetland soils has primarily focused on bacteria responsible for methanogenesis, denitrification, and sulfate reduction. There has been less work on taxonomic groups such as those responsible for nitrogen fixation, or aerobic processes such as nitrification. Work on general community composition and on wetland mycorrhizal fungi is particularly sparse. The general goal of microbial research has been to understand how microbial groups respond to the environment. There has been relatively little work done on the interactions among environmental controls over process rates, environmental constraints on microbial activities and community composition, and changes in processes at the ecosystem level. Finding ways to link process-based and biochemical or gene-based assays is becoming increasingly important as we seek a mechanistic understanding of the response of wetland ecosystems to current and future anthropogenic perturbations. We discuss the potential of new approaches, and highlight areas for further research.

Temporal variation in microbial communities is critical for sustainable utilization of marine biological resources and ecological restoration. However, microbial communities in China’s Bohai Sea remain inadequately characterized. This study employed high-throughput sequencing to characterize temporal–spatial variations in microbial communities within surface water and bottom sediment between June and August. A distinct temporal zone emerged in the sediments in August, characterized by low dissolved oxygen, bottom water acidification, and elevated concentrations of TN, NO3−, PO43−, and DOC. Furthermore, temporal variation exerted a stronger influence on microbial community. August induced a significant decline in aerobic bacteria and an increase in anaerobes. Crucially, a substantial increase in ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), coupled with a decrease in denitrifying bacteria, likely contributed to observed NO3− accumulation. Furthermore, complex alterations in sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) populations suggested potential impacts on sulfur cycling. This study provides critical insights for temporal–spatial variations in the microbial communities of the Bohai Sea, and provides a reference for developing effective coastal health indicators and further microbe resource exploration.

Microbial communities involved in electricity generation from sulfide oxidation in a microbial fuel cell

As an indispensable part of rhizosphere microorganisms, fungi participate in the processes of soil and rhizosphere element cycle and the degradation of pollutants in soil through self metabolism, and have huge potential in protecting tomato from abiotic and biological stresses. Tomato is one of the main varieties in the global trade of vegetables and fruits. In recent years, the planting area of tomato has continued to expand. The simple and intensive planting combined with high temperature and wet environmental conditions has facilitated the growth and breeding of diseases and pests, which has led to a sharp decline in tomato production. In addition, excessive use of chemicals and fertilizers has led to environmental pollution, which has led to a decline in tomato quality, and has caused huge losses to China’s vegetable economy. In this experiment, the rhizosphere soil of several common tomato diseases was used as research materials, and ITS sequencing was carried out for rhizosphere soil fungi by using high-throughput sequencing analysis. The operational taxon units (OTUs), alpha diversity, beat diversity and community structure were analyzed.

IntroductionPoplar (Populus spp.) is widely recognized as an ideal model system for studying plant-microbial interactions due to its rapid growth, genetic tractability, and ecological importance in afforestation programs. Leveraging these advantages, we investigated how poplar cultivation reshapes soil microbial communities and their nutrient cycling functions. Although plant roots are known to profoundly influence microbial community structure and functionality, comprehensive studies systematically linking poplar-induced microbiome shifts to nutrient cycling remain limited.MethodsHere, we employed an integrative approach combining metagenomic sequencing with soil nutrient analyses to assess poplar-induced changes in microbial community and metabolic activities at the root-soil interface.ResultsOur analyses revealed three major findings: (1) poplar cultivation significantly altered the composition of microbial communities—including bacteria, fungi, and archaea—and reduced the complexity of microbial interaction networks, as revealed by co-occurrence analysis; (2) poplar cultivation enhanced microbial genetic potential related to degradation pathways for starch, lignin, and aromatic compounds, as well as carbon (C) fixation, while suppressing cellulose/hemicellulose decomposition; and (3) soil nutrient cycling processes involving nitrogen (N), phosphorus (P), and sulfur (S) were reprogrammed through changes in both gene abundance (e.g., nifH, pqqC, aprA) and nutrient availability (e.g., NO3-, P). Moreover, specific microbial taxa showed strong correlations with these functional shifts, i.e., Bacteroidota correlated with P metabolism in roots/soil, Actinobacteria and Firmicutes with organic C turnover, and Gemmatimonadetes and Nitrospirae with nitrate cycling dynamics.DiscussionBy integrating poplar’s roles as both a model species and a driver of ecological change, this study elucidates how afforestation shapes soil ecosystems through complex plant-microbe-environment interactions. These findings provide critical insights for sustainable land management strategies.

Simple SummaryNormally, researchers use feces or rectal swabs to characterize a gut microbiome, but because there is significant spatiotemporal variation across different intestinal segments there are marked differences in composition and function of microbiomes among various gut sites. Hence, a consensus has not been reached on the location for sampling for gut microbial metagenome sequencing. This study provides a comparative perspective on gut microbial function that takes into account different sampling resources when conducting a metagenomic sequence analysis, highlighting the differences in the choice of a gut microbiome sampling site, and investigating whether feces and rectal swab samples are efficient proxies for gut microbiome sampling.When conducting metagenomic analysis on gut microbiomes, there is no general consensus concerning the mode of sampling: non-contact (feces), noninvasive (rectal swabs), or cecal. This study aimed to determine the feasibility and comparative merits and disadvantages of using fecal samples or rectal swabs as a proxy for the cecal microbiome. Using broiler as a model, gut microbiomes were obtained from cecal, cloacal, and fecal samples and were characterized according to an analysis of the microbial community, function, and resistome. Cecal samples had higher microbial diversity than feces, while the cecum and cloaca exhibited higher levels of microbial community structure similarity compared with fecal samples. Cecal microbiota possessed higher levels of DNA replicative viability than feces, while fecal microbiota were correlated with increased metabolic activity. When feces were excreted, the abundance of antibiotic resistance genes like tet and ErmG decreased, but some antibiotic genes became more prevalent, such as fexA, tetL, and vatE. Interestingly, Lactobacillus was a dominant bacterial genus in feces that led to differences in microbial community structure, metabolism, and resistome. In conclusion, fecal microbiota have limited potential as a proxy in chicken gut microbial community studies. Thus, feces should be used with caution for characterizing gut microbiomes by metagenomic analysis.

The metagenomic method directly sequences and analyses genome information from microbial communities. The main computational tasks for metagenomic analyses include taxonomical and functional structure analysis for all genomes in a microbial community (also referred to as a metagenomic sample). With the advancement of Next Generation Sequencing (NGS) techniques, the number of metagenomic samples and the data size for each sample are increasing rapidly. Current metagenomic analysis is both data- and computation- intensive, especially when there are many species in a metagenomic sample, and each has a large number of sequences. As such, metagenomic analyses require extensive computational power. The increasing analytical requirements further augment the challenges for computation analysis. In this work, we have proposed Parallel-META 2.0, a metagenomic analysis software package, to cope with such needs for efficient and fast analyses of taxonomical and functional structures for microbial communities. Parallel-META 2.0 is an extended and improved version of Parallel-META 1.0, which enhances the taxonomical analysis using multiple databases, improves computation efficiency by optimized parallel computing, and supports interactive visualization of results in multiple views. Furthermore, it enables functional analysis for metagenomic samples including short-reads assembly, gene prediction and functional annotation. Therefore, it could provide accurate taxonomical and functional analyses of the metagenomic samples in high-throughput manner and on large scale.

Soil processes such as decomposition are mainly performed by soil biota. Although, soils worldwide are extremely biodiverse, the relationship between decomposers (fauna and microorganisms) and ecosystem function is poorly understood. Collembola are abundant and ubiquitous microarthropods that are found in terrestrial ecosystems. They, directly or indirectly, impact the amount of biomass and influence the activity of microbial communities. However, despite the functional role they play in belowground food webs, the interactions between natural assemblages of soil microbes and Collembola receive little attention. This study, conducted in microcosm conditions, examines the effects of two distinct natural assemblages of functional groups of Collembola (ep- and euedaphic) upon microbial communities using PLFA markers and their associated soil functions (e.g., enzymatic activities and C mineralization rate) over a two-month period. Our principal objective was to determine whether different functional groups of Collembola had varying effects on microbial soil community abundance, structure and activity, resulting in potentially important effects on ecosystem processes. Our findings show that the interactions of the functional groups of Collembola with microbial communities vary significantly whether they are alone or combined. A distinct response in the composition of the microbial communities was found at the end of the 2-month period. The communities were significantly different from each other in terms of PLFA marker composition. We found that the epedaphic species were related to and promoted Gram+ bacteria whereas euedaphic species were related to Gram- bacterial markers. This had further repercussions on soil function, such as nutrient recycling. Combining both functional groups did not lead to a complementary effect on soil microbial properties, with a drastically different outcome between the first and the second month of the experiment. Additional research dealing with the interactions between decomposers using natural assemblages will help to predict the functional outcomes of soil biota structure and composition.

BackgroundA key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as ‘dead zones’. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface.ResultsCompared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation.ConclusionsThese novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses upon oxygenation of dead zones. Moreover, these results highlight that microbial responses, and therefore ultimately remediation efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane.

Metagenomics can be used to obtain sequence information on putative genes in a microbial community. However, it is difficult to identify genes with specific functions among the numerous predicted genes. In this study, we attempted to identify genes induced in cultured microbes by the addition of saccharides using metagenomic and metatranscriptomic analyses. A mixture of arabinoxylan and its derived oligosaccharides was used as the inducer in this study. Some genes were highly induced in the presence of additive saccharides and formed gene clusters for the utilization of additive saccharides, suggesting that metatranscriptomic and metagenomic analyses are useful for analyzing carbohydrate-responsive genes in microbial communities and screening novel carbohydrate-active enzymes.

Abstract. Climate change can strongly alter soil microbial functioning via plant–microbe interactions, often with important consequences for ecosystem carbon and nutrient cycling. Given the high degree of intraspecific trait variability in plants, it has been hypothesized that genetic shifts within plant species yield a large potential to control the response of plant–microbe interactions to climate change. Here we examined if sea-level rise and plant genotype interact to affect soil microbial communities in an experimental coastal wetland system, using two known genotypes of the dominant salt-marsh grass Elymus athericus characterized by differences in their sensitivity to flooding stress – i.e., a tolerant genotype from low-marsh environments and an intolerant genotype from high-marsh environments. Plants were exposed to a large range of flooding frequencies in a factorial mesocosm experiment, and soil microbial activity parameters (exo-enzyme activity and litter breakdown) and microbial community structure were assessed. Plant genotype mediated the effect of flooding on soil microbial community structure and determined the presence of flooding effects on exo-enzyme activities and belowground litter breakdown. Larger variability in microbial community structure, enzyme activities, and litter breakdown in soils planted with the intolerant plant genotype supported our general hypothesis that effects of climate change on soil microbial activity and community structure can depend on plant intraspecific genetic variation. In conclusion, our data suggest that adaptive genetic variation in plants could suppress or facilitate the effects of sea-level rise on soil microbial communities. If this finding applies more generally to coastal wetlands, it yields important implications for our understanding of ecosystem–climate feedbacks in the coastal zone.