From Soil to Surface: Exploring the Impact of Green Infrastructure on Microbial Communities in the Built Environment

Tidally influenced, saltwater marsh construction projects are being completed in Louisiana to combat coastal erosion and land loss, as well as to restore critical fisheries and counteract ecosystem injuries caused by oil spills and other anthropogenic activities. Historically, metrics of success for restored marshes have been based on the amount of aboveground biomass, survival of planted vegetation, and recruitment of local endemic versus invasive species. The microbial communities responsible for cycling nutrients within restored soils are not typically evaluated. Therefore, we investigated microbial community structure, biomass, and diversity in marsh soils that had been created from nearby dredge material over the past 10 years in the Lake Hermitage, West Point a La Hache area, and compared the results to those from natural marsh soils from Bay Batiste, as determined using phospholipid fatty acid (PLFA) and gas chromatography/mass spectrometry (GC/MS) techniques and from 16S rRNA gene profiles. Soils were collected from two depths (0-2 cm and 8-10 cm) from four sampling locations along a 100-m transect that extended inland from the coastline. Soil organic carbon content and soil pH were consistently lower at restored sites compared to natural marshes. Natural marsh soil microbial diversity strongly correlated with the biomass of typical marsh plants (e.g., Spartina alterniflora, Juncus roemerianus), whereas restored soil diversity correlated to higher Paspalum spp. (crowngrass) and Schoenoplectus pungens (common bulrush) biomass. Created soils had higher overall microbial diversity, but natural marsh soils had at least twice as much PLFA biomass than the created marshes at the shallow depth and 10X more biomass at the deeper depth. Biomass estimates ranged from below detectable levels to 6 x104 pmol PLFA gdw−1, with shallower soils from all sites exhibiting higher biomass (average 104 pmol PLFA gdw-1) compared to deeper soils (average 103 pmol PLFA gdw-1). Diverse PLFA profiles were observed. Shallow soils were dominated by terminally-branched and midchain-branched saturates that are indicative of Gram-positive microorganisms and actinomycetes. The shallow soils contained polyunsaturates indicative of phototrophs. Deeper soil profiles were dominated by monounsaturates associated with Gram-negative bacteria and sulfate- and metal-reducing bacteria. These monounsaturates contained on average 7% of the total PLFA profile as cyclopropyl fatty acids, which likely indicated anaerobic processes and the presence of nutritional stress. The shallow natural marsh soils exhibited more mid-branched saturates, branched monounsaturates, and polyunsaturates, whereas the shallow created marsh soils had more terminally-branched saturates. In the deeper soils, the natural marshes exhibited more terminally-branched saturates and monounsaturates, but the created marshes contained more saturates. GC/MS analyses of dimethyl disulfide derivatizations revealed shifts in microorganisms, as indicated by the types and bonding positions of monounsaturates, and the changes in the presence/absence of methanotrophic populations within the soils, which was also reflected in the 16S rRNA gene profiles. From these results, the microbial communities from the created marsh soils were different than the natural soil communities, and may reflect not being the best desired outcome for marsh restoration. With time, the expectation would be that created marsh above and belowground microbial diversity and biomass would begin to mimic natural marshes, but continued monitoring through time will be necessary to understand how these linkages develop and affect basic soil processes, nutrient cycling, and recruitment and sustenance of higher organisms like fish or crustaceans.

Microbial diversity is one important factor which controls agroecosystem productivity and quality. Microbial diversity is critical to ecosystem functioning due to its specificity in processes for which microbes are responsible. The presence of diverse soil microbes, bacteria, fungi, and archaea plays a critical role in cycling of major elements (C, N, P) which helps to maintain good soil health. These microbes help in maintaining soil structure, reduce susceptibility to pests and diseases, and eliminate hazardous substances from soil. In this review we addressed two significant questions concerning soil health: (1) how microbial diversity and community structure most effectively describe soil health and can be used as indicators and (2) how can soil health assessed by such indicators be improved or maintained? A summary of available techniques to characterize microbial community structure and diversity is provided, and information pertaining to strategies that can improve microbial diversity in relation to soil health by adopting suitable agricultural practices to sustain soil and crop productivity is furnished. These techniques include those for structural profiling, functional profiling, and other tools being used to assess microbial community diversity and their management through agricultural practices for improving the quality of soil and enhancing the crop productivity. Healthy soil supports high microbial diversity, activity, fertility, nutrient cycling, and disease-suppressive abilities. There is a considerable interest in understanding the nutrient cycles that regulates C, N, and P (carbon, nitrogen, phosphorus) exchange between the soil and atmosphere and how this exchange responds into tropical agroecosystem functioning under diverse edapho-climatic conditions.

Predictive microbial ecology

In recent years, the frequency and intensity of anthropogenic wildfires have drastically increased, significantly altering terrestrial ecosystems worldwide. These fires not only devastate vegetative cover but also impact soil environments and microbial communities, affecting ecosystem structure and function. The extent to which fire severity, soil depth, and their interaction influence these effects remains unclear, particularly in Pinus tabulaeformis forests. This study investigated the impact of wildfire intensity and soil stratification on soil physicochemical properties and microbial diversity within P. tabulaeformis forests in North China. Soil samples were collected from different fire severity zones (Control, Light, Moderate, High) and depths (topsoil: 0-10 cm; subsoil: 10-20 cm). Analyses included measurements of soil pH, organic carbon (SOC), total nitrogen (TN), and other nutrients. Microbial diversity was assessed using 16S rRNA gene sequencing. Our findings revealed significant variations in soil pH, SOC, TN, and other nutrients with fire severity and soil depth, profoundly affecting microbial community composition and diversity. Soil pH emerged as a critical determinant, closely linked to microbial α-diversity and community structure. We found that fire severity significantly altered soil pH (p = 0.001), pointing to noteworthy changes in acidity linked to varying severity levels. Topsoil microbial communities primarily differentiated between burned and unburned conditions, whereas subsoil layers showed more pronounced effects of fire severity on microbial structures. Analysis of bacterial phyla across different fire severity levels and soil depths revealed significant shifts in microbial communities. Proteobacteria consistently dominated across all conditions, indicating strong resilience, while Acidobacteriota and Actinobacteriota showed increased abundances in high-severity and light/moderate-severity areas, respectively. Verrucomicrobiota were more prevalent in control samples and decreased significantly in fire-impacted soils. Chloroflexi and Bacteroidota displayed increased abundance in moderate and high-severity areas, respectively. Correlation analyses illustrated significant relationships between soil environmental factors and dominant bacterial phyla. Soil organic carbon (SOC) showed positive correlations with total nitrogen (TN) and alkaline hydrolysable nitrogen (AN). Soil pH exhibited a negative correlation with multiple soil environmental factors. Soil pH and available phosphorus (AP) significantly influenced the abundance of the phylum Myxococcota. Soil water content (WC) significantly affected the abundances of Acidobacteriota and Actinobacteriota. Additionally, ammonium nitrogen (NH4 +-N) and nitrate nitrogen (NO3 --N) jointly and significantly impacted the abundance of the phylum Chloroflexi. This study highlights the significant long-term effects of anthropogenic wildfires on soil microenvironment heterogeneity and bacterial community structure in P. tabulaeformis forests in North China, 6 years post-fire. Our findings demonstrate that fire severity significantly influences soil pH, which in turn affects soil nutrient dynamics and enhances microbial diversity. We observed notable shifts in the abundance of dominant bacterial phyla, emphasizing the critical role of soil pH and nutrient availability in shaping microbial communities. The results underscore the importance of soil stratification, as different soil layers showed varying responses to fire severity, highlighting the need for tailored management strategies. Future research should focus on long-term monitoring to further elucidate the temporal dynamics of soil microbial recovery and nutrient cycling following wildfires. Studies investigating the roles of specific microbial taxa in ecosystem resilience and their functional contributions under varying fire regimes will provide deeper insights. Additionally, exploring soil amendments and management practices aimed at optimizing pH and nutrient availability could enhance post-fire recovery processes, supporting sustainable ecosystem recovery and resilience.

Soil microbial communities, including bacteria and fungi, play a crucial role in nutrient cycling processes such as carbon sequestration, nitrogen transformation, and phosphate mobilization. Despite their importance, the dynamics of microbial communities in tropical soils remain poorly understood. This study investigates the composition, functional potential, and nutrient profiles of microbial communities across various land-use types, including forests, agricultural farms, parks, and golf courses. Soil samples were analyzed to assess microbial abundance, diversity, and nutrient content.Bacterial abundances were significantly higher than fungal abundances across all soil types, with agricultural soils showing bacterial abundances that were one order of magnitude greater than those in other soil types. Fungal diversity was influenced by land use, with forest soils dominated by decomposers such as Basidiomycota and Ascomycota, which enhance organic matter turnover and contribute to soil carbon dynamics. In contrast, agricultural soils were enriched in Zygomycota, known for their roles in nutrient cycling and plant growth promotion under conditions of elevated nutrient availability.Distinct clustering of bacterial communities was observed using principal coordinate analysis, with agricultural soils forming unique clusters separate from other soil types. Organic farming practices were found to support bacterial and fungal communities more similar to natural ecosystems compared to conventional farming. Agricultural soils exhibited higher nutrient levels and microbial biomass due to intensive fertilization, while the forest, park and golf course soils displayed variability in microbial diversity and nutrient content driven by vegetation maturity and management practices. Mature forest soils were characterized by signature taxa such as Gaiella (bacteria) and Trichoderma (fungi), indicative of healthy soil ecological conditions, while agricultural soils were dominated by Bacillus and Paenibacillus, associated with nutrient cycling and pathogen suppression.These findings highlight the influence of land use and management practices on microbial and fungal community composition, functional potentials, and nutrient cycling. The implications are significant for understanding nutrient concentration in runoff and their impacts on water quality, particularly under climate change scenarios involving temperature increases and intensified rainfall and length of dry periods.

Application of organic fertilizer improves microbial community diversity and alters microbial network structure in tea (Camellia sinensis) plantation soils

The microbiome inhabiting animal skin plays a crucial role in host fitness by influencing both the composition and function of microbial communities. Environmental factors, including climate, significantly impact microbial diversity and the functional attributes of these communities. However, it remains unclear how specific climatic factors affect amphibian skin microbial composition, community function, and the relationship between these two aspects. Understanding these effects is particularly important because amphibians are poikilotherms and, thus, more susceptible to temperature fluctuations. Here, we investigated the skin microbiome of the rhacophorid tree frog Polypedates megacephalus across different climatic regimes using 16S rRNA gene sequencing. Skin swab samples were collected from nine populations of P. megacephalus adults in the Guangxi region, China. The majority of the core microbiota were found to belong to the genus Pseudomonas. Our findings indicate that microbial community diversity, composition, and function are associated with changes in climatic conditions. Specifically, the taxonomic and functional diversity of the skin microbiome increased in response to higher climate variability, particularly in temperature fluctuations. Additionally, the functional traits of microbial communities changed in parallel with shifts in community diversity and composition. The significant correlations of the functional redundancy index with climatic factors suggest that environmental filtering driven by climate change impacts microbial community functional stability. These results highlight the critical influence of climatic factors on amphibian skin microbiomes and offer new insights into how microbial composition and function contribute to host adaptation in varying environmental conditions.IMPORTANCEThis study is important in understanding the association between climate variability, microbial diversity, and host adaptation in amphibians, which are particularly vulnerable to environmental changes due to their poikilothermic nature. Amphibians rely on their skin microbiome for key functions like disease resistance, yet little is known about how climate fluctuations impact these microbial communities. By analyzing the microbiome of Polypedates megacephalus across different climatic regimes, our analysis reveals that warmer climates could reduce the microbial diversity and community functional redundancy, indicating the functional stability of skin microbiome could be susceptible to climate variability, particularly in hosts adapted to relatively cooler conditions. These findings highlight the potential ecological consequences of climate change and emphasize the need to integrate microbiome health into amphibian conservation strategies.

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

ABSTRACTProphages are often involved in host survival strategies and contribute toward increasing the genetic diversity of the host genome. Prophages also drive horizontal propagation of various genes as vehicles. However, there are few retrospective studies contributing to the propagation of antimicrobial resistance (AMR) and virulence factor (VF) genes by prophage. We extracted the complete genome sequences of seven pathogens, including ESKAPE bacteria and Escherichia coli from a public database, and examined the distribution of both the AMR and VF genes in prophage-like regions. We found that the ratios of AMR and VF genes greatly varied among the seven species. More than 70% of Enterobacter cloacae strains had VF genes, but only 1.2% of Klebsiella pneumoniae strains had VF genes from prophages. AMR and VF genes are unlikely to exist together in the same prophage region except in E. coli and Staphylococcus aureus, and the distribution patterns of prophage types containing AMR genes are distinct from those of VF gene-carrying prophage types. AMR genes in the prophage were located near transposase and/or integrase. The prophage containing class 1 integrase possessed a significantly greater number of AMR genes than did prophages with no class 1 integrase. The results of this study present a comprehensive picture of AMR and VF genes present within, or close to, prophage-like elements and different prophage patterns between AMR- or VF-encoding prophage-like elements.IMPORTANCE Although we believe phages play an important role in horizontal gene transfer in exchanging genetic material, we do not know the distribution of the antimicrobial resistance (AMR) and/or virulence factor (VF) genes in prophages. We collected different prophage elements from the complete genome sequences of seven species—Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae, and Escherichia coli—and characterized the distribution of antimicrobial resistance and virulence genes located in the prophage region. While virulence genes in prophage were species specific, antimicrobial resistance genes in prophages were highly conserved in various species. An integron structure was detected within specific prophage regions such as P1-like prophage element. Maximum of 10 antimicrobial resistance genes were found in a single prophage region, suggesting that prophages act as a reservoir for antimicrobial resistance genes. The results of this study show the different characteristic structures between AMR- or VF-encoding prophages.

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.

Cattle grazing management affects soil microbial diversity and community network complexity in the Northern Great Plains

Arbuscular mycorrhizal fungi outcompete fine roots in determining soil multifunctionality and microbial diversity in a desert ecosystem

Soil microbial species diversity and distribution of microbial communities are vital for soil and crop health, nutrient cycling, availability, and subsequent plant growth. These soil dynamics are highly influenced and altered by various soil management practices, inputs, and agricultural techniques. In the present study, the effects of chemical and organic management practices on soil microbial diversity and community structure were examined and compared using amplicon sequencing of the 16S and ITS regions. Two contrasting soil samples were selected from each crop fields at the International Rice Research Institute-South Asia Regional Centre (IRRI-SARC) in Varanasi: one field followed conventional chemical fertilizer inputs, while the other implemented natural farming practices, including tillage, on-farm crop residue management, and water management. Soil samples from each field were analyzed for bacterial and fungal diversity. Our findings showed that the two differently managed soils exhibited distinct microbial community compositions, with the organically managed soil exhibiting a higher diversity of decomposer bacteria and fungi, showing 40 unique elements in organic soil samples and 19 in chemically managed soil. Natural farming practices also demonstrated a higher relative abundance of bacterial and fungal phyla. Our results emphasize the significance of sustainable soil management techniques, suggesting that organic inputs can increase soil microbial diversity and richness. The functional roles of these microbial communities in soil ecosystems and their potential impact on crop yield and nutrient cycling warrant further study.

Tidal wetland reclamation could profoundly alter ecological function and ecosystem service provision, but its impacts on sediment microbial communities and functions remain poorly understood. We investigated spatial and seasonal patterns of greenhouse gases (GHGs) production response to land-use changes in mangrove wetlands and unraveled the underlying mechanisms by integrating environmental parameters and microbial communities. Land-use changes substantially reduced microbial community richness and diversity and shaped their composition. Converting mangrove to drier orchard and vegetable field reduced sediment organic matter, carbon GHGs production rates, and microbial network complexity and stability, while increased N2O production rates. Converting mangrove to chronically flooded aquaculture pond increased sediment CH4 production rates, but reduced N2O and CO2 production rates. Although increasing anthropogenic disturbance in aquaculture pond have reduced microbial community richness and diversity compared to native mangrove wetland, they have increased complexity of species associations resulting in a more complex and stable network. Microbial community richness and network complexity and stability were strongly related to CH4 and N2O production rates, but not significantly associated with CO2 production rates, suggesting microbial community richness, network complexity and stability are better predictors of the specialized soil/sediment functions CH4 and N2O production). Therefore, preserving microbial “interaction” could be important to mitigate the negative effects of microbial community richness and diversity loss caused by human activities. Furthermore, as the residual bait accumulation is a severe issue in aquaculture activities, we especially focused on the influence of bait input at time scale through a 90-day incubation experiment, aiming to observe temporal variations of physicochemical properties, sediment microbial community, and GHGs production in response to different amounts of bait input. The results showed that dissolved oxygen of overlying water was profoundly decreased owing to bait input, while dissolved organic carbon of overlying water and several sediment properties (e.g., organic matter, sulfide, and ammonium) varied in reverse patterns. Meanwhile, bait input strongly altered microbial compositions from aerobic, slow-growing, and oligotrophic to anaerobic, fast-growing, and copiotrophic. Moreover, both GHGs production and global warming potential were enhanced by bait input, implying that aquaculture ecosystem is an important hotspot for global GHGs emission. Overall, bait input triggered quick responses of physicochemical properties, sediment microbial community, and GHGs production, followed by long-term resilience of the ecosystem. Future research should comprehensively consider microbial diversity, species composition and interaction strength, functions, and environmental conditions to accurately predict soil/sediment functioning and emphasize the necessity of sustainable assessment and effective management.

Remote sensing ecological index (RSEI) affects microbial community diversity in ecosystems of different qualities