Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community ...effects during a bioremediation-related organic carbon disturbance. Subsurface sediment, partitioned into 22 flow-through columns, was stimulated in situ by the addition of acetate as a carbon and electron donor source. This drove the system into a new transient biogeochemical state characterized by iron reduction and enriched Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After approximately 1 month conditions favoured sulfate reduction, and were accompanied by a substantial increase in the relative abundance of Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum. Two subsets of four to five columns each were switched from acetate to lactate amendment during either iron (earlier) or sulfate (later) reduction. Hence, subsets had significantly different founding communities. All lactate treatments exhibited lower relative abundances of Desulfotomaculum and Bacteroidetes, enrichments of Clostridiales and Psychrosinus species, and a temporal succession from highly abundant Clostridium sensu stricto to Psychrosinus. Regardless of starting point, lactate-switch communities followed comparable structural trajectories, whereby convergence was evident 9 to 16 days after each switch, and significant after 29 to 34 days of lactate addition. Results imply that neither the founding community nor neutral processes influenced succession following perturbation.
Variability in the activity and composition of soil microbial communities may have important implications for the suite of microbially-derived ecosystem functions upon which agricultural systems ...rely, particularly organic agriculture. An on-farm approach was used to investigate microbial communities and soil carbon (C) and nitrogen (N) availability on 13 organically-managed fields growing Roma-type tomatoes, but differing in nutrient management, across an intensively-managed agricultural landscape in the Central Valley of California. Soil physicochemical characteristics, potential activities of nine soil enzymes involved in C, N, phosphorus (P), and sulfur (S) cycling, and fatty acid methyl esters (FAMEs) were measured during the growing season and evaluated with multivariate approaches. Soil texture and pH in the 0–15 cm surface layer were similar across the 13 fields, but there was a three-fold range of soil C and N as well as substantial variation in inorganic N and available P that reflected current and historical management practices. Redundancy analysis showed distinct profiles of enzyme activities across the fields, such that C-cycling enzyme potential activities increased with inorganic N availability while those of N-cycling enzymes increased with C availability. Although FAMEs suggested that microbial community composition was less variable across fields than enzyme activities, there were slight community differences that were related to organic amendments (manure vs. composted green waste). Overall, however, the general similarity among fields for particular taxonomic indicators, especially saprophytic fungi, likely reflects the high disturbance and low complexity in this landscape. Variation in potential enzyme activities was better accounted for with soil physicochemical characteristics than microbial community composition, suggesting high plasticity of the resident microbial community to environmental conditions. These patterns suggest that, in this landscape, differences in organic agroecosystem management have strongly influenced soil nutrients and enzyme activity, but without a major effect on soil microbial communities. The on-farm approach provided a wide range of farming practices and soil characteristics to reveal how microbially-derived ecosystem functions can be effectively manipulated to enhance nutrient cycling capacity.
•Soil microbial community activity and composition was investigated in 13 organic fields.•C-cycling enzyme activities increased with inorganic N availability.•N-cycling enzyme activities increased with C availability.•Microbial community composition was differentiated by organic amendment applied.
In this study, Moringa oleifera leaves (MOL) were fermented with or without pyroligneous acid (PA) for 3, 7, 14, and 30 days. PA addition enhanced the contents of acetic acid and true protein ...(P < 0.01) and decreased pH (P < 0.01) and the contents of coliform bacteria, nonprotein nitrogen (P < 0.01), and ammonium nitrogen (P < 0.01). With the addition of PA, the abundance of Lactobacillus increased, but the abundance of Enterobacter decreased. A total of 754 metabolites were identified. In the MOL fermented with PA, the contents of apigenin, arbutin, 2-methoxy-4-vinyl phenol, and 4-methoxy cinnamic acid increased, while the content of skatole decreased compared with the contents for the MOL fermented without PA. The detected metabolites were correlated with bacterial communities, especially Lactobacillus and Weissella. In conclusion, the addition of PA improves the fermentation quality and protein preservation and affects the microbial communities and metabolites of fermented MOL.
•Pyroligneous acid (PA) improved the fermentation quality of Moringa oleifera leaves.•PA increased the abundance of Lactobacillus and decreased that of Enterobacter.•PA changed the metabolites during the fermentation of M. oleifera leaves.•The metabolites were strongly correlated with Lactobacillus and Weissella.
Unraveling the drivers controlling community assembly is a central issue in ecology. Although it is generally accepted that selection, dispersal, diversification and drift are major community ...assembly processes, defining their relative importance is very challenging. Here, we present a framework to quantitatively infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93-0.99), precision (0.80-0.94), sensitivity (0.82-0.94), and specificity (0.95-0.98) on simulated communities, which are 10-160% higher than those from the entire community-based approach. Application of iCAMP to grassland microbial communities in response to experimental warming reveals dominant roles of homogeneous selection (38%) and 'drift' (59%). Interestingly, warming decreases 'drift' over time, and enhances homogeneous selection which is primarily imposed on Bacillales. In addition, homogeneous selection has higher correlations with drought and plant productivity under warming than control. iCAMP provides an effective and robust tool to quantify microbial assembly processes, and should also be useful for plant and animal ecology.
Hydraulic fracturing (HF) has substantially boosted global unconventional hydrocarbon production but has also introduced various environmental and operational challenges. Understanding the ...interactions between abundant and diverse microbial communities and chemicals, particularly polymers used for proppant delivery, thickening, and friction reduction, in HF water cycles is crucial for addressing these challenges. This review primarily examined the recent studies conducted in China, an emerging area for HF activities, and comparatively examined studies from other regions. In China, polyacrylamide (PAM) and its derivatives products became key components in hydraulic fracturing fluid (HFF) for unconventional hydrocarbon development. The microbial diversity of unconventional HF water cycles in China was higher compared to North America, with frequent detection of taxa such as Shewanella, Marinobacter, and Desulfobacter. While biodegradation, biocorrosion, and biofouling were common issues across regions, the mechanisms underlying these microbe-polymer interactions differed substantially. Notably, in HF sites in the Sichuan Basin, the use of biocides gradually decreased its efficiency to mitigate adverse microbial activities. High-throughput sequencing proved to be a robust tool that could identify key bioindicators and biodegradation pathways, and help select optimal polymers and biocides, leading to more efficient HFF systems. The primary aim of this study is to raise awareness about the interactions between microorganisms and polymers, providing fresh insights that can inform decisions related to enhanced chemical use and biological control measures at HF sites.
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•Hydraulic fracturing created environment for intense interactions between microbial communities and polymers.•Biodegradation, biocorrosion, and biofouling have impacted production efficiency and environmental health.•Advanced materials and methods are needed to monitor and assess chemical and microbial community changes.
Micro- and nano-plastics (MPs/NPs) have emerged as a global pollutant, yet their impact on the root environment of plants remains scarcely explored. Given the widespread pollution of phthalate esters ...(PAEs) in the environment due to the application of plastic products, the co-occurrence of MPs/NPs and PAEs could potentially threaten the growth medium of plants. This study examined the combined effects of polystyrene (PS) MPs/NPs and PAEs, specifically dibutyl phthalate and di-(2-ethylhexyl) phthalate, on the chemical properties and microbial communities in a wheat growth medium. It was observed that the co-pollution with MPs/NPs and PAEs significantly increased the levels of oxalic acid, formic acid, and total organic carbon (TOC), enhanced microbial activity, and promoted the indigenous input and humification of dissolved organic matter, while slightly reducing the pH of the medium solution. Although changes in chemical indices were primarily attributed to the addition of PAEs, no interaction between PS MPs/NPs and PAEs was detected. High-throughput sequencing revealed no significant change in microbial diversity within the media containing both PS MPs/NPs and PAEs compared to the media with PS MPs/NPs alone. However, alterations in energy and carbohydrate metabolism were noted. Proteobacteria dominated the bacterial communities in the medium solution across all treatment groups, followed by Bacteroidetes and Verrucomicrobia. The composition and structure of these microbial communities varied with the particle size of the PS in both single and combined treatments. Moreover, variations in TOC, oxalic acid, and formic acid significantly influenced the bacterial community composition in the medium, suggesting they could modulate the abundance of dominant bacteria to counteract the stress from exogenous pollutants. This research provides new insights into the combined effects of different sizes of PS particles and another abiotic stressor in the wheat root environment, providing a critical foundation for understanding plant adaptation in complex environmental conditions.
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•Co-pollution of MPs/NPs and PAEs increased the content of oxalic acid and formic acid.•PS MPs/NPs and PAEs impacted the function of the bacterial community.•The composition and structure of these microbial communities varied with the size of PS.•The content of TOC and formic acid were related to shifts in bacterial community composition.
The distinctive environmental attributes of the Southern Ocean underscore the indispensability of microorganisms in this region. We analyzed 208 samples obtained from four separate layers (Surface, ...Deep Chlorophyll Maximum, Middle, and Bottom) in the neighboring seas of the Antarctic Peninsula and the Cosmonaut Sea to explore variations in microbial composition, interactions and community assembly processes. The results demonstrated noteworthy distinctions in alpha and beta diversity across diverse communities, with the increase in water depth, a gradual rise in community diversity was observed. In particular, the co-occurrence network analysis exposed pronounced microbial interactions within the same water mass, which are notably stronger than those observed between different water masses. Co-occurrence network complexity was higher in the surface water mass than in the bottom water mass. Yet, the surface water mass exhibited greater network stability. Moreover, in the phylogenetic-based β-nearest taxon distance analyses, deterministic processes were identified as the primary factors influencing community assembly in Antarctic microorganisms. This study contributes to exploring diversity and assembly processes under the complex hydrological conditions of Antarctica.
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•Disparities in water mass between the Antarctic Peninsula and the Cosmonaut Sea•Reveals microbial spatial variation across large-scale Antarctic water masses•Indicates an increase in the α-diversity of microbial with depth•Microbial interactions in each water mass are stronger than those with various masses.•Homogeneous selection is the main community assembly process of microorganisms.
•35 years of inorganic fertilizer and manure amendment alter the soil bacterial and archaeal community.•pH and NO3− concentration played important roles in shaping the community structures.•Inorganic ...fertilizers decrease soil bacterial and archaeal diversity.•The incorporation of inorganic fertilizer and manure increase soil bacterial and archaeal diversity.
Black soil is common in northeast China and plays an important role in Chinese crop production. However, in the past three decades, inappropriate use of fertilizer has caused a sequence of agroecological issues. The objective of this research was to evaluate the effect of long-term fertilizer on the microbial communities in black soil. The soil was subjected to four fertilization regimes: without fertilizer (CK); manure (M); nitrogen, phosphorus and potassium inorganic fertilizer (NPK); and inorganic fertilizers with manure (MNPK). The soil pH was decreased by inorganic fertilizers and increased by manure. Quantitative PCR analysis of microbial community size and Illumina platform-based analysis of the V4 16S rRNA gene region were performed to characterize soil microbial abundance and to compare community structure and diversity. Microbial community size was enhanced by the incorporation of inorganic fertilizer and manure. Microbial diversity was decreased by inorganic fertilizer and increased by the incorporation of inorganic fertilizer and manure. The predominate phyla in all samples were Proteobacteria (29.39–33.48%), Acidobacteria (13.14–16.25%) and Actinobacteria (9.32–10.77%). The relative abundance of different classes significantly differed among the different treatments, especially MNPK and NPK. Acidobacteria and Deltaproteobacteria were relatively stable in organic fertilizer treated soil. Gammaproteobacteria, Alphaproteobacteria and Betaproteobacteria were sensitive to all the fertilization regimes. Comparatively, Spartobacteria was stable in response to fertilization practices. Principal coordinate analysis indicated that microbial communities were primarily clustered into three groups: CK and M were clustered together; MNPK was improved by manure and separated from NPK. Shannon and Simpson indexes were significantly correlated with soil pH and the concentrations of available phosphorus and total phosphorus. Redundancy analysis indicates that microbial communities were closely positively correlated with soil nitrate nitrogen concentration (P=0.002) and pH (P=0.002). These results indicate that inorganic fertilizer plus manure increased microbial size and diversity and changed microbial composition.
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•Helical impeller improves mixing & reduces stratification vs. pitched-blade impeller.•Pitched-blade impeller diminishes bacterial diversity, no effect on methanogens.•Pitched-blade ...impeller enhances digestate dewaterability in lab reactors.•Impeller geometry – a new perspective to enhance digestate dewaterability.
The efficiency of anaerobic digestion (AD) processes is intricately tied to mixing quality. This research investigates the influence of two impeller types, namely a helical ribbon impeller (HRI) and a pitched-blade impeller (PBI), on key aspects of AD. The investigation encompassed mixing dynamics, methane production, microbial communities, and the previously unexplored impact on digestate dewaterability. Results show that agitation with the PBI exhibited stratification, with bottom layer total solids (TS) values of 3.1% for the PBI and 2.6% for the HRI. Nevertheless, methane yield remained unchanged, averaging 286 LN/kg volatile solids (VS)added. Slower mixing with the HRI achieved more uniform mixing and reduced energy requirements. Additionally, impeller type significantly affected digestate dewaterability, leading to a 3.8% increase in TS of the dewatered sludge when using the PBI. These findings highlight the importance of considering mixing not only for methane production and reduced maintenance but also for achieving optimal digestate dewaterability.
The detrimental effects of microplastics (MPs) on soil microbial and elemental raise significant environmental concerns. The potential of remediation with biochar to mitigate these negative impacts ...remains an open question. The remediation effects of biochar derived from corn and cotton straw on MPs concerning soil microorganisms and element cycling were investigated. Specifically, biochar induced substantial remediations in microbial community structure following MP exposure, restoring and fortifying the symbiotic network while exerting dominance over microbial community changes. A combined treatment of biochar and MPs exhibited a noteworthy increase in the abundance of NH4+, NO3−, and available phosphorous by 0.46–2.1 times, reversing the declining trend of dissolved organic carbon, showing a remarkable increase by 0.36 times. This combined treatment also led to a reduction in the abundance of the nitrogen fixation gene nifH by 0.46 times, while significantly increasing the expression of nitrification genes (amoA and amoB) and denitrification genes (nirS and nirK) by 22.5 times and 1.7 times, respectively. Additionally, the carbon cycle cbbLG gene showed a 2.3-fold increase, and the phosphorus cycle gene phoD increased by 0.1-fold. The mixed treatment enriched element-cycling microorganisms by 4.8–9.6 times. In summary, the addition of biochar repaired the negative effects of MPs in terms of microbial community dynamics, element content, gene expression, and functional microbiota. These findings underscore the crucial role of biochar in alleviating the adverse effects of MPs on microbial communities and elemental cycling, providing valuable insights into sustainable environmental remediation strategies.
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•Negative impact of microplastics on soil microbial communities was confirmed.•Negative impact of microplastics on soil element cycles was confirmed.•Biochar played a leading role when coexisting with microplastics.•Biochar mitigated microbes and element cycles changes caused by microplastics.
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