Microbial Community Patterns Research Articles

Improved resolution of microbial diversity in deep-sea surface sediments using PacBio long-read 16S rRNA gene sequencing

ABSTRACT 16S rRNA gene sequencing is the gold standard for identifying microbial diversity in environmental communities. The Illumina short-read platform is widely used in marine environment studies due to its cost-effectiveness and high accuracy, but its limited read length restricts taxonomic identification mainly to genus or family levels. Recently, the PacBio long-read sequencing platform was developed. This method has exceptional base-level resolution exceeding 99%, thereby effectively mitigating the challenges associated with high error rates commonly observed in long-read sequencing technologies. However, few studies have compared the PacBio long-read and Illumina short-read platforms in marine deep-sea sediments. Here, the PacBio long-read and Illumina short-read platforms were compared with samples collected from the deep-sea surface sediments from the cold seep in the Shenhu area of the South China Sea offshore Pearl River Estuary. Comparisons revealed a more comprehensive taxonomic identification, α-diversity, and β-diversity by PacBio long-reads. The PacBio long-read platform exhibited higher classified rates and classified taxonomy at all levels, particularly at the species level. The PacBio long-read platform was also more accurate at capturing fine spatial-scale variations in microbial communities in sediments. Our studies will facilitate the selection of 16S rRNA sequencing platforms for investigating fine spatial-scale patterns in microbial communities in deep-sea surface sediments and serve as a crucial methodological reference for future studies on microbial diversity. IMPORTANCE The PacBio long-read platform, with its exceptional base-level resolution exceeding 99%, has advanced our comprehension of deep-sea microbial diversity. By comparing microbial community analyses conducted using the Illumina short-read and PacBio long-read sequencing platforms, we have provided an enhanced understanding of fine spatial-scale patterns in microbial community diversity with depth across a deep-sea sediment core, as well as methodological insights that will be valuable for future research in this field.

The role of gut microbiota in a generalist, golden snub-nosed monkey, adaptation to geographical diet change

Changes in diet causing ecological stress pose a significant challenge to animal survival. In response, the gut microbiota, a crucial part of the host’s digestive system, exhibits patterns of change reflective of alterations in the host’s food component. The impact of temporal dietary shifts on gut microbiota has been elucidated through multidimensional modeling of both food component and macronutrient intake. However, the broad distribution of wild generalist and the intricate complexity of their food component hinder our capacity to ascertain the degree to which their gut microbiota assist in adapting to spatial dietary variations. We examined variation in patterns of the gut microbial community according to changes in diet and in a colobine monkey with a regional variable diet, the golden snub-nosed monkey (Rhinopithecus roxellana). Specifically, we analyse the interactions between variation in food component, macronutrient intake and the gut microbial community. We compared monkeys from four populations by quantifying food component and macronutrient intake, and by sequencing 16S rRNA and the microbial macro-genomes from the faecal samples of 44 individuals. We found significant differences in the diets and gut microbial compositions, in nutrient space and macronutrient intake among some populations. Variations in gut microbiota composition across distinct populations mirror the disparities in macronutrient intake, with a notable emphasis on carbohydrate. Geographical differences in the diet among of golden snub-nosed monkey populations will result in macronutrient intake variation, with corresponding differences in macronutrient intake driving regional differences in the compositions and abundances of gut microbiota. Importantly, the gut microbiota associated with core digestive functions does not vary, with the non-core gut microbiota fluctuating in response to variation in macronutrient intake. This characteristic may enable species heavily reliant on gut microbiota for digestion to adapt to diet changes. Our results further the understanding of the roles gut microbiota play in the formation of host dietary niches.

Effects of Different Wheat Varieties on Soil Bacterial and Fungal Communities

ABSTRACTThe diversity and stability of soil microbial communities are indispensable components for maintaining the functions and services of agricultural ecosystems and play crucial roles in wheat production. However, the effects of different wheat varieties on soil microbial diversity, network complexity, stability, and assembly mechanisms remain largely unexplored. To bridge this research gap, we conducted field experiments in Chuzhou, China, to study the yield and soil microbial community composition of six different wheat varieties. The soil bacterial and fungal communities were investigated using high‐throughput sequencing of the 16S rRNA and ITS gene regions. Our findings indicated that, compared to common wheat, high‐yielding and disease‐resistant (HD) wheat increased both bacterial and fungal α‐diversity by regulating soil nitrogen and phosphorus concentrations, significantly affecting community structure (Adonis, p < 0.001). HD wheat significantly altered the co‐occurrence network patterns of soil microbial communities. Network analyses revealed that HD wheat increased the complexity of fungal networks while exhibiting the opposite trend for bacterial networks. However, both the bacterial and fungal networks demonstrated increased stability. Furthermore, HD wheat may increase microbial migration rates, influencing assembly processes by promoting stochastic processes in bacterial and fungal communities. Overall, this study provides valuable insights into the ecological functions and driving factors of soil microbes, offering information for the development of ecological management strategies to achieve sustainable wheat cultivation and improve soil quality. Furthermore, HD wheat significantly modified the co‐occurrence network patterns of the soil microbial communities. Network analysis revealed increased fungal network complexity in HD wheat, whereas bacterial networks showed the opposite trend. However, both the bacterial and fungal networks exhibited enhanced stability. Additionally, HD wheat likely increased microbial migration rates, influencing assembly processes by promoting stochastic processes in both bacterial and fungal communities. Overall, this study provides valuable insights into the ecological functions and driving factors of soil microbes, providing information for the development of ecological management strategies to achieve sustainable wheat cultivation and improve soil quality.

Seasonal variations of microbial communities and viral diversity in fishery-enhanced marine ranching sediments: insights into metabolic potentials and ecological interactions

BackgroundThe ecosystems of marine ranching have enhanced marine biodiversity and ecological balance and have promoted the natural recovery and enhancement of fishery resources. The microbial communities of these ecosystems, including bacteria, fungi, protists, and viruses, are the drivers of biogeochemical cycles. Although seasonal changes in microbial communities are critical for ecosystem functioning, the current understanding of microbial-driven metabolic properties and their viral communities in marine sediments remains limited. Here, we employed amplicon (16S and 18S) and metagenomic approaches aiming to reveal the seasonal patterns of microbial communities, bacterial-eukaryotic interactions, whole metabolic potential, and their coupling mechanisms with carbon (C), nitrogen (N), and sulfur (S) cycling in marine ranching sediments. Additionally, the characterization and diversity of viral communities in different seasons were explored in marine ranching sediments.ResultsThe current study demonstrated that seasonal variations dramatically affected the diversity of microbial communities in marine ranching sediments and the bacterial-eukaryotic interkingdom co-occurrence networks. Metabolic reconstruction of the 113 medium to high-quality metagenome-assembled genomes (MAGs) was conducted, and a total of 8 MAGs involved in key metabolic genes and pathways (methane oxidation - denitrification - S oxidation), suggesting a possible coupling effect between the C, N, and S cycles. In total, 338 viral operational taxonomic units (vOTUs) were identified, all possessing specific ecological characteristics in different seasons and primarily belonging to Caudoviricetes, revealing their widespread distribution and variety in marine sediment ecosystems. In addition, predicted virus-host linkages showed that high host specificity was observed, with few viruses associated with specific hosts.ConclusionsThis finding deepens our knowledge of element cycling and viral diversity in fisheries enrichment ecosystems, providing insights into microbial-virus interactions in marine sediments and their effects on biogeochemical cycling. These findings have potential applications in marine ranching management and ecological conservation.DRyDF7ykR-XALqAtu34uZtVideo

Depth-dependent effects of forest diversification on soil functionality and microbial community characteristics in subtropical forests

Soil microbes are critical to the maintenance of forest ecosystem function and stability. Forest diversification, such as monocultures versus mixed forests stands, can strongly influence microbial community patterns and processes, as well as their role in soil ecosystem multifunctionality, such as in subtropical forest ecosystems. However, less is known about these patterns and processes vary with soil depth. Here, we investigated the results of an eight-year forest diversification field experiment comparing the soil ecosystem multifunctionality, bacterial and fungal community assembly, and network patterns in mixed versus monoculture plantations along vertical profiles (0–80 cm depth) in a subtropical region. We found that the introduction of broadleaf trees in coniferous monocultures led to enhanced synergies between multiple functions, thus improving soil multifunctionality. The effects of mixed plantations on the functional potential in top soils were greater than in deep soils, especially for carbon degradation genes (apu, xylA, cex, and glx). Microbial community assembly in the top layer, particularly in mixed plantations, was dominated by stochastic processes, whereas deterministic were more important in the deep layer. Soil microbial network complexity and stability were higher in the top layer of mixed plantations, but in the deep layer was monoculture. Interestingly, the changes in microbial communities and multifunctionality in the top layer were mainly related to variation in nutrients, whereas those in the deep were more influenced by soil moisture. Overall, we reveal positive effects of mixed forest stands on soil microbial characteristics and functionality compared to that of monocultures. Our findings highlighted the importance of enhancing functional diversity through the promotion of tree species diversity, and managers can better develop forest management strategies to promote soil health under global change scenarios.

Alpine SOC and Microbial Community Assembly Were Buffered Through Soil Pore Structure Along an Altitudinal Gradient

ABSTRACTElevation changes influence various environmental factors including cloudiness, atmospheric density, and temperature. Previous studies on the effects of elevation on microbial communities and soil organic carbon (SOC) yielded inconsistent results. This study tried to reveal the distribution patterns of microbial communities and SOC concentrations, as well as their interactions with soil structure along an elevational gradient in the alpine region. We investigated six typical ecosystems along an elevational gradient on the north‐eastern Qinghai‐Tibet Plateau. Phospholipid fatty acid (PLFA) analysis and X‐ray computed tomography (CT) methods were used to quantify microbial abundance and pore structure of soils, respectively. The results demonstrated that SOC content and total PLFAs peaked in the meadow ecosystem. In the subsoil, total PLFAs, fungal, and bacterial PLFAs followed the U‐shape pattern with increasing elevation. In both topsoils and subsoils, the surface area density of pores increased with elevation, and it was found to be positively correlated with SOC and microbial abundance. Soil structure mainly affects the input and adsorption of root nutrients by altering the pore surface area, thereby regulating the enrichment of microorganisms. The impact of pore structure on microbes were more obvious in the topsoil than in the subsoil. Interactions among pore structure, soil properties, and environmental factors jointly affects the microbial communities, demonstrating that elevation indirectly affects microbial communities through soil resource regulation.

Bacterial microbiome and their assembly processing in two sympatric desert rodents (Dipus sagitta and Meriones meridianus) from different geographic sources

Abstract The microbiome of mammals has profound effects on host fitness, but the process, which drives the assembly and shift of mammalian microbiome remains poorly understood. To explore the patterns of small mammal microbial communities across host species and geographical sites and measure the relative contributions of different processes in driving assembly patterns, 2 sympatric desert rodent species (Dipus sagitta and Meriones meridianus) were sampled from 2 geographically distant regions, which differed in the environment, followed by 16S rRNA gene sequencing. The microbiomes differed significantly between D. sagitta and M. meridianus, and linear mixed modeling (LMM) analysis revealed that microbial diversity was mostly affected by species rather than the environment. For each rodent species, the microbiome diversity and structure differed across geographical regions, with individuals from lower rainfall environments exhibiting greater diversity. The null modeling results suggested dispersal limitation and ecological drift rather than differential selective pressures acting on the microbiome. In addition, each group had a different core genus, suggesting that the taxonomic composition of the microbiome was shaped most strongly by stochastic processes. Our results suggest that variation in the microbiome between hosts, both within and among geographic rodent populations, is driven by bacterial dispersal and ecological drift rather than by differential selective pressures. These results elucidated the diversity patterns and assembly processes of bacterial microbiomes in small desert mammals. Deciphering the processes shaping the assembly of the microbial community is a premise for better understanding how the environment-host-microbe interactions of mammals are established and maintained, particularly in the context of increased environmental disturbances and global changes.

Assembly and co-occurrence pattern of microbial communities in bulk and rhizosphere soils of Pinus elliottii plantations on sandy lands in China

Assembly and co-occurrence pattern of microbial communities in bulk and rhizosphere soils of Pinus elliottii plantations on sandy lands in China

Disclosing the key role of Fe/As/Cu in community co-occurrence and microbial recruitment in metallurgical ruins

Mining activities have led to the persistent presence of substantial heavy metals at metallurgical sites. However, the impact of long-term and complex heavy metal pollution in metallurgical ruins on the structure and spatial shift of microbiome remains unclear. In this study, we focused on various types of metallurgical sites to uncover the occurrence of heavy metals in abandoned mines and the response patterns of microbial communities. The results indicate that mining activities have caused severe exceedances of multiple heavy metals, with AsBio, CuBio, and FeBio being the primary factors affecting community structure and function. Co-occurrence network analyses suggest that several genera, including Ellin6515, Cupriavidus, Acidobacteria genus RB41, Vicinamibacteraceae, Blastococcus, and Sphingomonas, may play significant roles in the synergistic metabolism of communities responding to Fe-Cu-As stress. Although random dispersal contributed to community migration, null models emphasized that variable selection predominates in the spatial turnover of community composition. Additionally, metagenomic prediction (PICRUSt2) identified key genes involved in stress and detoxification strategies of heavy metals. The composite heavy metal stress strengthened the relationship between network structure and the potential function of the community, along with critical ecosystem functions. Our findings demonstrated that microbial interactions were crucial for ecosystem management and the ecological consequences of heavy metal pollution remediation.

Biological Decline of Alfalfa Is Accompanied by Negative Succession of Rhizosphere Soil Microbial Communities.

The growth and biological decline of alfalfa may be linked to the rhizosphere microbiome. However, plant-microbe interactions in the rhizosphere of alfalfa and associated microbial community variations with stand age remain elusive. This study explored the successional pattern of rhizosphere microbial communities across different aged alfalfa stands and its relationship with alfalfa decline. Rhizosphere soils were collected from 2- and 6-year-old alfalfa stands. Control soils were collected from interspaces between alfalfa plants in the same stands. Soil bacterial and fungal communities were characterized by 16S and ITS rRNA gene sequencing, respectively. Specific microbial taxa colonized the rhizosphere soils, but not the control soils. The rhizosphere-specific taxa mainly included potentially beneficial genera (e.g., Dechloromonas, Verrucomicrobium) in the young stand and harmful genera (e.g., Peziza, Campylocarpon) in the old stand. Alfalfa roots regulated soil microbial communities by selective promotion or inhibition of distinct taxa. The majority of time-enriched taxa were reported as harmful fungi, whose relative abundances were negatively correlated with plant traits. Time-depleted taxa were mostly known as beneficial bacteria, which had relative abundances positively correlated with plant traits. The relative abundances of functional bacterial genes associated with vancomycin biosynthesis, zeatin biosynthesis, and amino acid metabolism trended lower in rhizosphere soils from the old stand. An upward trend was observed for fungal pathogens and wood saprotrophs with increasing stand age. The results suggest that root activity drives the negative succession of rhizosphere microbial communities during alfalfa decline in old stands.

Soil Characteristics and Response Mechanism of the Microbial Community in a Coal–Grain Compound Area with High Groundwater Levels

Coal mining has led to escalating ecological and environmental issues in significant coal and grain production areas, posing a severe danger to food security. This study examines the disturbance patterns of soil factors and microbial communities in coal and grain production areas, and attempts to understand the impact of subsidence and water accumulation stress on soil characteristics and microbial communities in coal mining subsidence areas with high subsidence levels. Five specific regions of Zhao Gu Yi Mine, situated in Henan Province and under the ownership of Jiaozuo Coal Group, were chosen. Aside from the control group (CK), the study blocks situated in the coal mining subsidence zones consisted of perennial subsidence ponding (PSP), seasonal subsidence ponding (SSP), the neutral zone (NZ), and the horizontal deformation zone (HDZ). The soil nutrient indices and the stoichiometric properties of soil C, N, and P were assessed on the surface of each block. The organization of the soil microbial community was identified using high-throughput sequencing. The findings indicate that: 1. Substantial disparities exist in soil properties and microbial community structure between the subsidence and non-subsidence zones. The levels of soil organic mater (SOM), total nitrogen (TN), total phosphorus (TP), available nitrogen (AN), and available phosphorus (AP) all decrease to different extents in the subsidence area. Additionally, the coal mining subsidence waterlogged area exhibits higher levels compared to the coal mining subsidence non-waterlogged area. Conversely, the soil water content (SWC), C/N ratio, C/P ratio, and N/P ratio all increase to varying degrees. 2. Regarding the composition of the community, the presence of Proteobacteria is considerably greater in the non-water-logged area of coal mining subsidence (NZ, HDZ) compared to the water-logged area and control group (p < 0.05). The prevalence of Firmicutes in the subsidence water area was substantially greater compared to both the subsidence non-waterlogged area and the control group (p < 0.05). The prevalence of Gemmatimonadota is markedly greater in the waterlogged area of mining subsidence compared to the non-waterlogged area and CK (p < 0.05). The Ascomycota population reached its highest value in the neutral zone (NZ), which was significantly greater than the values observed in the seasonal subsidence ponding (SSP) and perennial subsidence ponding (PSP) regions (p < 0.05). On the other hand, the Rozellomycota population had its highest value in the SSP region, which was significantly greater than the values observed in the other regions (p < 0.05). 3. The abundance and variety of soil bacteria and fungi, as well as their important populations, are associated with different levels of soil characteristics. The primary elements that influence the alteration of microbial communities are soil nutrients and soil water content. The presence of coal mine subsidence and water accumulation has a notable impact on the properties of the soil in the surrounding area. This study offers a scientific foundation for reclaiming land affected by subsidence caused by coal mining in regions where coal and grain production are the dominant industries.

Species pool and local assembly processes drive β diversity of ammonia-oxidizing and denitrifying microbial communities in rivers along a latitudinal gradient.

Both regional species pool and local community assembly mechanism drive the microbial diversity patterns across geographical gradients. However, little has been done to separate their effects on the β diversity patterns of microbial communities involved in nitrogen (N) cycling in river ecosystems. Here, we use high-throughput sequencing of the archaeal amoA, bacterial amoA, nirK, and nirS genes, null model, and neutral community model to distinguish the relative importance of species pool and local assembly processes for ammonia-oxidizing and denitrifying communities in river wetlands along a latitudinal gradient in eastern China. Results indicated that the β diversity of the nirS-type denitrifying community co-varied with γ diversity and environmental heterogeneity, implying that regional species pool and heterogeneous selection explained variation in β diversity. However, the β diversity of ammonia-oxidizing and nirK-type denitrifying communities did not correlate with γ diversity and environmental heterogeneity. The continuous hump distribution of β deviation along the latitudinal gradient and the lower species dispersal rate indicated that the dispersal limitation shaped the variation in β diversity of ammonia-oxidizing and nirK-type denitrifying communities. Additionally, biotic interactions drove ammonia-oxidizing and nirS-type denitrifying communities by influencing species co-occurrence patterns. Our study highlights the importance of regional species pool and local community assembly processes in shaping geographical patterns of N-cycling microorganisms and extends knowledge of their adaptability to a continuously changing environment on a large scale.

Microbiome signature of different stages of hypoxia event in Wonmun Bay

We investigated how microbial communities associated with different hypoxic stages respond to environmental changes across three water depths in Wonmun Bay, South Korea. Analysis of temperature, salinity, dissolved oxygen (DO), and nutrient concentrations revealed prominent seasonal shifts and strong stratification during summer hypoxia. Metabarcoding of prokaryotic 16 S rRNA genes and phototrophic eukaryotic chloroplasts along with quantitative PCR (qPCR) revealed variations in the abundance and composition of these communities. Chloroplast 16 S sequences in May were dominated by land plants (93% of Embryophyta), contrasting with the diverse phytoplankton taxa detected in other months. The water communities in May also had higher total microbial abundance than other months but significantly lower alpha diversity. These results suggest a major influence of freshwater discharge on water communities, pre-conditioning for hypoxia events by promoting organic matter decomposition coupled with DO consumption in bottom water. Subsequently, distinct microbial communities were observed across depths during hypoxia in June and July, while less variability was detected among different depths in September and later months when hypoxia events disappeared. Principal Coordinate analysis (PCoA) demonstrated the distinct patterns of microbial communities in May, June, and July from other months. Both sulfur-oxidizing and sulfate-reducing bacteria (SRB) were prevalent in June while the increase of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) was observed in mid and bottom water in July. This data suggests the intricate interaction between sulfur and nitrogen-cycling microbes during the hypoxia events in Wonmun Bay. In conclusion, this study provides valuable insights into the microbial community responses to the varying environmental conditions at different stages of hypoxia events in eutrophic coastal ecosystems.

Response characteristics of soil microorganisms under strong disturbance conditions in the riparian zone of the three Gorges reservoir Area

The normal operation of the Three Gorges Reservoir, which involves periodic water storage and discharge, has led to strong disturbances in environmental conditions that alter soil microbial habitats in the riparian zones. Riparian zones are an important part of controlling pollution in the Three Gorges Reservoir area, since they act as a final ecological barrier that intercepts pollutants. Meanwhile, monitoring the health of microbial communities in the riparian zone is crucial for maintaining the ecological security of the reservoir area. We specifically investigate the Daning River, which are tributaries of the Three Gorges Reservoir and have typical riparian zones. Soil samples from these areas were subjected to high-throughput sequencing of 16S rRNA genes and 18S rRNA genes, in order to obtain the characteristics of the present microbial communities under strong disturbances in the riparian zones. We studied the characteristics and distribution patterns of microbial communities and their relationship with soil physicochemical properties. The study results indicate that microbial communities exhibit high diversity and evenness, and spatial heterogeneity is present. The ASV dataset contains many sequences not assigned to known genera, suggesting the presence of new fungal genera in the riparian zone. Redundancy analysis (RDA) revealed that pH and NH4+\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${NH}_{4}^{+}$$\\end{document}-N were the primary environmental factors driving bacterial community variation in the riparian zone, while pH, total carbon (TC) content, and NO3-\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${NO}_{3}^{-}$$\\end{document}-N were identified as the main drivers of soil archaeal community variation.

Unraveling the spatio-temporal dynamics of soil and root-associated microbiomes in Texas olive orchards

Understanding the structure and diversity of microbiomes is critical to establishing olives in non-traditional production areas. Limited studies have investigated soil and root-associated microbiota dynamics in olives across seasons or locations in the United States. We explored the composition and spatiotemporal patterns of the olive-associated microbial communities and specificity in two niches (rhizosphere and root endosphere), seasons (spring, summer, and fall), and domains (bacteria and fungi) in the microbiome of the olive cultivar Arbequina across three olive orchards in Texas. Phylum Proteobacteria, followed by Actinobacteriota, dominated the bacterial populations in the rhizosphere and endosphere. Rubrobacter and Actinophytocola were dominant taxa in the rhizosphere and root endosphere at the genus level. Among fungal communities, phylum Ascomycota was prevalent in the rhizosphere and endosphere, while members of the Chaetomiaceae family outnumbered other taxa in the root endosphere. As per the alpha diversity indices, the rhizosphere at Moulton showed much higher richness and diversity than other places, which predicted a significant difference in rhizosphere between locations for bacterial diversity and richness. There was no significant variation in the bacterial diversity in the niches and the fungal diversity within the root endosphere between locations. Beta diversity analysis confirmed the effect of compartments—in influencing community differences. Microbial diversity was apparent within the endosphere and rhizosphere. The seasons influenced only the rhizosphere fungal diversity, contrasting the bacterial diversity in either niche. The research provided a comprehensive overview of the microbial diversity in olive trees' rhizosphere and root endosphere. The abundance and composition of OTUs associated with the rhizosphere soil of Arbequina suggest its role as a source reservoir in defining the potential endophytes.

Climate determines diversity but not abundance of nitrogen-cycling microorganisms in rivers across a latitudinal gradient

ABSTRACT A central goal in microecology is to understand the ecological factors shaping spatial patterns of microbial communities and the underlying mechanisms. However, the biogeographical patterns of microbial functional groups involved in nitrogen cycling (e.g., nitrifiers and denitrifiers) and their drivers at a large scale remain poorly understood. In this study, we evaluated the geographical distributions of nitrifiers and denitrifiers in riparian rhizosphere soils, riparian bulk soils, and channel sediments of 30 river regions along a latitudinal gradient from 21.8°N to 45.1°N across eastern China. We found that the diversity of nitrifiers and denitrifiers exhibited a gradual latitudinal gradient, in direct contrast to no significant changes observed for their abundance along the same latitudinal gradient. Statistical analyses suggested that climatic factors (mean annual temperature and mean annual precipitation) were the major drivers for the diversity of nitrifiers and denitrifiers, whereas soil properties were the key environmental factors shaping the abundance of nitrifiers and denitrifiers. These results provide new insights into the biogeographical distributions and ecological drivers for nitrogen-cycling microorganisms in river ecosystems at a large scale and can help us to improve simulation models of the nitrogen cycle for accurately predicting the diversity of nitrogen-cycling microbes under ongoing climate changes.

Groundwater flow regime shapes nitrogen functional traits by affecting microbial community assembly processes in the subsurface

The complex nitrogen (N) cycle in groundwater systems is affected by both biological and environmental factors. The interactions between hydrogeological conditions and the microbial community assembly processes that impact N-cycling processes remain poorly understood. We explored the assembly patterns of N-cycling microbial communities along the groundwater flow path. The environmental heterogeneity in different hydrological phases increased along the flow path (mean Ed: 0.16–0.49), accompanied by different microbial community assembly patterns. The assembly patterns that engaged in dissimilatory nitrate reduction to ammonium (DNRA) and denitrification changed across the water-sediment phases. Nitrifying microorganisms in the discharge area were mainly influenced by heterogeneous selection (41–69 %), and were closely correlated with dissolved oxygen (DO) concentrations. Homogeneity along flow-through increased stochastic assemblies, such as downstream drift of anammox bacterial (AnAOB) communities. Thus, the N removal pathway changed from “nitrification-denitrification” in the recharge area to “partial nitrification-anammox” in the discharge area. The increasing environmental heterogeneity brought more deterministic assembly patterns of N-cycling communities, linked to higher community turnover along the groundwater flow path. This study indicated that groundwater flow regime determined microbial community assembly patterns, providing valuable insight into the response of N transitions to environmental variations in groundwater systems.

Riboflavin-induced microbial succession for enhanced tellurite reduction in wastewater treatment

Tellurite is a common component of industrial wastewater; thus, its efficient removal is crucial for environmental protection and wastewater treatment. Although the efficiency is low, the activated sludge process (ASP) is frequently used to treat wastewater by reducing tellurite (Te(Ⅳ)) to harmless elemental tellurium (Te(0)). Riboflavin is a biostimulant that when added to ASP can significantly shape the structure of microbial communities and improve the efficiency of treating telluride-containing wastewater. However, the underlying biological mechanism remains unclear. Herein, two groups—control and biostimulation—of sequencing batch reactors (SBRs) were constructed and run under the same conditions. In the control group (CG), only tellurite was added, whereas biostimulation group (BS) was treated with tellurite and riboflavin. After adding riboflavin, chemical oxygen demand, tellurite removal rates, and extracellular polymeric substance generation increased. The 16 S rRNA high-throughput sequencing results revealed that the succession of microbial communities was effectively promoted in the ASP by riboflavin treatments and that telluride-reducing bacteria—such as Sphingopyxis, Shinella, Brevundimonas, and Brucella—were significantly increased. Key topological properties suggested that riboflavin treatments changed the co-occurrence patterns of SBR microbial communities and strengthened microbial interactions, considerably improving the stability and efficiency of the tellurium-containing wastewater treatment system. In summary, we explored the effect of adding riboflavin to the ASP to stimulate the succession of sludge microbial communities for improved tellurite reduction. The findings of this research contribute to our understanding of the mechanism of riboflavin in optimizing wastewater treatment for removing recalcitrant pollutants.

Unveiling soil microbial community dynamics in desertification: A case study from the tianshan mountains, xinjiang

Microorganisms constitute the primary ecological group in desertified soil, driving soil biogeochemical cycles. Understanding their structure and diversity is crucial for the ecological restoration of desertification areas. This study focuses on the typical desert slopes in the eastern section of the northern foothills of the Tianshan Mountain in Xinjiang, China. It investigates changes in the main prokaryotic microbial community structure, including bacteria and archaea, and their relationship with environmental factors. Results show generally low soil water content, increasing with depth, and a weak alkaline nature with no significant vertical variations. While microbial communities do not distinctly respond to soil water content, there are noticeable variations in microbial diversity with clear stratification, negatively correlated with total organic carbon. Molecular ecological network analyses of five bare soil profiles in Xinjiang’s Hami Tianshan Desert reveal positive interactions among soil microorganisms in vertical layers. Surprisingly, the topsoil, despite having complex networks, shows low diversity and weak interconnectivity. Intriguingly, subsurface soils exhibit distinct molecular ecological networks similar to those found in ecological transition zones (These zones are characterized by rapid environmental shifts from one type to another), further highlighting significant ecological disparities between surface and subsurface soils. By analyzing the structure of soil microbial communities and their relationship with environmental factors on typical desert slopes in the Tianshan Mountains of Xinjiang, significant microbial ecological differences are found between surface and subsurface soils. Notably, in subsurface soils, microbial networks similar to those in ecological transition zones are discovered. These areas have complex microbial community structures and diverse ecological functions, providing new insights into the mechanisms of ecological restoration in desertified soils. Consequently, this study suggests that the vertical distribution patterns of microbial communities in bare desert soil areas differ from those in vegetated areas such as forests and grasslands. The interactions among species, the unique distribution of soil organic matter, and various physical factors are likely pivotal in the distribution patterns of microbial communities in bare desert soils. This research provides foundational theories and empirical support for the ecological restoration of bare desert soils.

Deciphering taxonomic and functional patterns of microbial communities associated with the tiger tail seahorse (Hippocampus comes).

Gaining insight into the diversity, structure, and metabolic functions of microbial communities is essential for understanding their roles in host health and ecosystem dynamics. However, research on the seahorse-associated microbiome remains limited, despite these threatened fish facing increasing human pressures worldwide. Here, we explored the microbial diversity and metabolic functions of the skin and gut of the tiger tail seahorse (Hippocampus comes) and its surrounding environment using shotgun metagenomics and bioinformatics. Members of the Pseudomonadota phylum were dominant in the skin microbiome, whereas Bacteroidota was dominant in the gut. Bacillota, Actinomycetota, and Planctomycetota were also detected in the seahorse-associated microbiome. Statistical analysis revealed significant differences (P < 0.01) in species diversity between skin and gut microbiomes, with members belonging to the Moraxellaceae family being dominant on the skin and the Bacteroidaceae family in the gut. Moreover, the surrounding environment (water or sediment) did not have a direct effect on the seahorse microbiome composition. The skin microbiome exhibited a higher abundance of functional genes related to energy, lipid, and amino acid metabolism as well as terpenoids and polyketides metabolism, xenobiotics biodegradation, and metabolism compared with the gut. Despite differences among classes, the total abundance of bacteriocins was similar in both gut and skin microbiomes, which is significant in shaping microbial communities due to their antimicrobial properties. A better knowledge of seahorse microbiomes benefits conservation and sustainable aquaculture efforts, offering insights into habitat protection, disease management, and optimizing aquaculture environments, thereby promoting seahorse health and welfare while minimizing environmental impact and enhancing aquaculture sustainability.NEW & NOTEWORTHY To the best of our knowledge, this study represents the first comprehensive examination of the taxonomic and functional patterns of the skin and gut microbiome in the tiger tail seahorse. These findings have the potential to significantly enhance our understanding of the seahorse-associated microbiome, thereby contributing to the prediction and control of bacterial infections in seahorses, which are a leading cause of high mass mortality rates in seahorse aquaculture and other fish species.