Microbial Community Shifts Research Articles

Emergence of rare and low abundant anaerobic gut Firmicutes is associated with a significant downfall of Klebsiella in human colon cancer

Gut bacterial dysbiosis has been linked to several gastrointestinal diseases, including deadly colorectal cancer (CRC), a leading cause of mortality in cancer patients. However, perturbation in gut bacteriome during colon cancer (CC, devoid of colorectal malignancy) remains poorly explored. Here, 16S rRNA gene amplicon sequencing was carried out for fecal DNA samples targeted to hypervariable V3–V4 region by employing MiSeq platform to explore the gut bacterial community shift in CC patients. While alpha diversity indices predicted high species richness and diversity, beta diversity showed marked gut bacterial compositional dissimilarity in CC versus healthy controls (HC, n = 10 each). We observed a significant (p < 0.05, Wilcoxon Rank-Sum test) emergence of low-abundant anaerobic taxa, including Parvimonas and Peptostreptococcus, in addition to Subdoligranulum, Coprococcus, Holdemanella, Solobacterium, Bilophila, Blautia, Dorea, Moryella and several unidentified taxa, mainly affiliated to Firmicutes, in CC patients. In addition, we also traced the emergence of putative probiotic taxon Slackia, belonging to Actinomycetota, in CC patients. The emergence of anaerobic Firmicutes in CC is accompanied by a significant (p < 0.05) decline in the Klebsiella, as determined through linear discriminant analysis effect size (LEfSe) and heat tree analyses. Shifts in core microbiome and variation in network correlation were also witnessed. Taken together, this study highlighted a significant and consistent emergence of rare anaerobic Firmicutes suggesting possible anaerobiosis driving gut microbial community shift, which could be exploited in designing diagnostic and therapeutic tools targeted to CC.

Soil organic matter priming: The pH effects.

Priming of soil organic matter (SOM) decomposition by microorganisms is a key phenomenon of global carbon (C) cycling. Soil pH is a main factor defining priming effects (PEs) because it (i) controls microbial community composition and activities, including enzyme activities, (ii) defines SOM stabilization and destabilization mechanisms, and (iii) regulates intensities of many biogeochemical processes. In this critical review, we focus on prerequisites and mechanisms of PE depending on pH and assess the global change consequences for PE. The highest PEs were common in soils with pH between 5.5 and 7.5, whereas low molecular weight organic compounds triggered PE mainly in slightly acidic soils. Positive PEs up to 20 times of SOM decomposition before C input were common at pH around 6.5. Negative PEs were common at soil pH below 4.5 or above 7 reflecting a suboptimal environment for microorganisms and specific SOM stabilization mechanisms at low and high pH. Short-term soil acidification (in rhizosphere, after fertilizer application) affects PE by: mineral-SOM complexation, SOM oxidation by iron reduction, enzymatic depolymerization, and pH-dependent changes in nutrient availability. Biological processes of microbial metabolism shift over the short-term, whereas long-term microbial community adaptations to slow acidification are common. The nitrogen fertilization induced soil acidification and land use intensification strongly decrease pH and thus boost the PE. Concluding, soil pH is one of the strongest but up to now disregarded factors of PE, defining SOM decomposition through short-term metabolic adaptation of microbial groups and long-term shift of microbial communities.

Measuring the Fate and Natural Attenuation Potential of a Viscous Marine Fuel on an Artificial Beach Mesocosm

Shoreline oiling poses a risk to coastal ecosystems and resources. Understanding the natural attenuation potential and impact of different sediment types is important for choosing appropriate intervention strategies and priority areas following a spill. Simulated IFO-40 oil spills on artificial beach mesocosms were carried out using different sediment types: sandy beach and sandy tidal flat, under low energy tidal cycles over a 5-day period. Chemical and biological analysis of leachate and sediment was conducted to understand the movement of oil through these mesocosms. Rapid oil movement from the oil slick to the surface sediment layer was observed in the sandy beach enclosures, while slower oil movement was observed in the sandy tidal flat enclosures. Increased hydrocarbon dissolution was observed in the sandy beach enclosures, marked by higher concentrations of low molecular weight n-Alkanes (C12 − 15) and naphthalenes (C0 − 3) in sandy beach leachate compared to sandy tidal flat samples. Despite the increase in hydrocarbons, there were no major shifts in microbial communities observed in the leachate and sediment compartments for either sediment type. Both prokaryote and microeukaryote communities differed between the two sediment types, with little overlap between dominant sequences. Our results indicate that limited oil penetration occurs within sandy tidal flat shorelines resulting in oil accumulation suggesting that sorbent or vacuuming could be used as emergency response to minimize the environmental and ecological impacts of spilled oil.

Deciphering the reduction of antibiotic resistance genes (ARGs) during medium-chain fatty acids production from waste activated sludge: Driven by inhibition of ARGs transmission and shift of microbial community

Medium-chain fatty acids (MCFAs) production from waste activated sludge (WAS) by chain extension (CE) is a promising technology. However, the effects and mechanisms of CE process on the fate of antibiotic resistance genes (ARGs) remain unclear. In this study, the results showed that the removal efficiency of ARGs was 81.15 % in CE process, suggesting its efficacy in reducing environmental risks. Further, the observed decrease in mobile genetic elements (MGEs) indicated that CE process restricted the horizontal gene transfer (HGT). Complementing this, the increase in soluble organic matters and extracellular 16 S rDNA confirmed that MCFAs production caused bacterial damage. Decreased intracellular ARGs and increased extracellular ARGs further revealed that MCFAs production impaired ARGs hosts, thereby limiting the vertical gene transfer (VGT) of ARGs. Shift of microbial community combined with co-occurrence network analysis demonstrated that functional bacteria without host potential for ARGs were enriched, but potential ARGs and MGEs hosts decreased, showing the role of functional bacterial phylogeny and selection pressure of MCFAs in reducing ARGs. Finally, partial least squares path model was used to systematic verify the mechanism of ARGs removal in CE process, which was attributed to the inhibition of ARGs transmission (HGT and VGT) and shift of microbial community.

Changes in chemical properties and microbial communities' composition of a forest litter-based biofertilizer produced through aerated solid-state culture under different oxygen conditions.

Fermented forest litter (FFL) is a bioproduct used as biofertilizer for several decades in Eastern Asia and Latin America. It is locally handcrafted by farmers in anaerobic conditions by fermenting forest litter added with agricultural by-products such as whey, cereal bran, and molasses. The aim of this study was to characterize the FFL process and product through gas and liquid chromatography analyses. It also provides some highlights on the influence of O2 on this solid-state culture. Under anoxic condition, a maximum CO2 production rate (CDPR) of 0.41mL/h∙g dry matter (dm) was reached after 8days. The main volatile organic compounds (VOCs) were ethanol and ethyl acetate, with a production rate profile similar to CDPR. After 21days of culture, no residual sucrose nor lactose was detected. Lactic and acetic acids reached 58.8mg/g dm and 10.2mg/g dm, respectively, ensuring the acidification of the matrix to a final pH of 4.72. A metabarcoding analysis revealed that heterolactic acid bacteria (Lentilactobacillus, Leuconostoc), homolactic acid bacteria (Lactococcus), and yeasts (Saccharomyces, Clavispora) were predominant. Predicted genes in the microbiome confirmed the potential link between detected bacteria and acids and VOCs produced. When O2 was fed to the cultures, final pH reached values up to 8.5. No significant amounts of lactic nor acetic acid were found. In addition, a strong shift in microbial communities was observed, with a predominance of Proteobacteria and molds, among which are potential pathogens like Fusarium species. This suggests that particular care must be brought to maintain anoxic conditions throughout the process.

Denaturing Gradient Gel Electrophoresis Approach for Microbial Shift Analysis in Thermophilic and Mesophilic Anaerobic Digestions.

To determine the evolution of microbial community and microbial shift under anaerobic processes, this study investigates the use of denaturing gradient gel electrophoresis (DGGE). In the DGGE, short- and medium-sized DNA fragments are separated based on their melting characteristics, and this technique is used in this study to understand the dominant bacterial community in mesophilic and thermophilic anaerobic digestion processes. Dairy manure is known for emitting greenhouse gases (GHGs) such as methane, and GHG emissions from manure is a biological process that is largely dependent on the manure conditions, microbial community presence in manure, and their functions. Additional efforts are needed to understand the GHG emissions from manure and develop control strategies to minimize the biological GHG emissions from manure. To study the microbial shift during anaerobic processes responsible for GHG emission, we conducted a series of manure anaerobic digestion experiments, and these experiments were conducted in lab-scale reactors operated under various temperature conditions (28 °C, 36 °C, 44 °C, and 52 °C). We examined the third variable region (V3) of the 16S rRNA gene fingerprints of bacterial presence in anaerobic environment by PCR amplification and DGGE separation. Results showed that bacterial community was affected by the temperature conditions and anaerobic incubation time of manure. The microbial community structure of the original manure changed over time during anaerobic processes, and the community composition changed substantially with the temperature of the anaerobic process. At Day 0, the sequence similarity confirmed that most of the bacteria were similar (>95%) to Acinetobacter sp. (strain: ATCC 31012), a Gram-negative bacteria, regardless of temperature conditions. At day 7, the sequence similarity of DNA fragments of reactors (28 °C) was similar to Acinetobacter sp.; however, the DNA fragments of effluent of reactors at 44 °C and 52 °C were similar to Coprothermobacter proteolyticus (strain: DSM 5265) (similarity: 97%) and Tepidimicrobium ferriphilum (strain: DSM 16624) (similarity: 100%), respectively. At day 60, the analysis showed that DNA fragments of effluent of 28 °C reactor were similar to Galbibacter mesophilus (strain: NBRC 10162) (similarity: 87%), and DNA fragments of effluent of 36 °C reactors were similar to Syntrophomonas curvata (strain: GB8-1) (similarity: 91%). In reactors with a relatively higher temperature, the DNA fragments of effluent of 44 °C reactor were similar to Dielma fastidiosa (strain: JC13) (similarity: 86%), and the DNA fragments of effluent of 52 °C reactor were similar to Coprothermobacter proteolyticus (strain: DSM 5265) (similarity: 99%). To authors' knowledge, this is one of the few studies where DGGE-based approach is utilized to study and compare microbial shifts under mesophilic and thermophilic anaerobic digestions of manure simultaneously. While there were challenges in identifying the bands during gradient gel electrophoresis, the joint use of DGGE and sequencing tool can be potentially useful for illustrating and comparing the change in microbial community structure under complex anaerobic processes and functionality of microbes for understanding the consequential GHG emissions from manure.

Heavy metals in a typical industrial area-groundwater system: Spatial distribution, microbial response and ecological risk

The environmental burden due to industrial activities has been quite observable in the last few years, with heavy metals (HMs) like lead, cadmium, and arsenic inducing serious perturbations to the microbial ecosystem of groundwater. Studies carried out in North China, a region known for interconnection of industrial and groundwater systems, sought to explore the natural mechanisms of adaptation of microbes to groundwater contamination. The results showed that heavy metals permeate from surface increased the diversity and abundance of microbial communities in groundwater, producing an average decrease of 40.84% and 34.62% in the relative abundance of Bacteroidetes and Proteobacteria in groundwater, respectively. Meanwhile, the key environmental factors driving the evolution of microbial communities shift from groundwater nutrients to heavy metals, which explained 50.80% of the change in the microbial community composition. Microbial indicators are more sensitive to HMs pollution and could accurately identify industrial area where HMs permeation occurred and other extraneous pollutants. The phylum Bacteroidetes could act as appropriate indicators for the identification. Significant genera that were identified, being Mesorhizobium, Clostridium, Bacillus and Mucilaginibacter, were found to play important roles in the microbial network in terms of the potential to assist in groundwater clean-up. Notably, pollution from heavy metals has diminished the effectiveness and resilience of microbial communities in groundwater, thereby heightening the susceptibility of these normally stable microbial ecosystems. These findings offer new perspectives on how to monitor and detect groundwater pollution, and provide scientific guidance for developing suitable remediation methods for groundwater contaminated with heavy metals. Future research is essential explore the application of metal-tolerant or resistant bacteria in bioremediation strategies to rehabilitate groundwater systems contaminated by HMs.

Effect of coastal hypoxia on bacterial diversity as elucidated through 16S rRNA amplicon sequencing

The formation of oxygen-depleted zones in the bottom waters is one of the most widespread phenomena in coastal areas. Upwelling episodes along India’s west coast due to the southwest monsoon increase biological productivity, further lowering the dissolved oxygen in the upwelled waters, which intensifies annually between June and October. Here, we have determined the changes in the microbial community in response to the varying oxygen levels and other physicochemical parameters at the Candolim Time Series Station using high-throughput sequencing. Amplicon Sequence Variants across all the samples collected in different seasons were mostly affiliated to the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, Chloroflexi, Firmicutes and Planctomycetes, with the most dominant being Proteobacteria (21-41%). Statistical analysis revealed that microbial diversity differed significantly with changing DO, ammonia, nitrate and nitrite concentrations during different seasons. The microbial community shift due to seasonal hypoxia results in the differential biogeochemical cycling of essential nutrients, with certain years seeing redox conditions up to sulphate reduction while certain years seeing only nitrogen loss. Future global warming scenarios will serve as a big challenge for understanding the role of microbial diversity and its implications in the cycling of natural elements.

Microbial response to a port fuel spill: Community dynamics and potential for bioremediation

Following a fuel leakage inside a Portuguese maritime port, we conducted parallel 30-day experiments using contaminated seawater and fuel, sampled five days after the incident. This study aimed to (i)survey the native microbial community response to the spilled fuel and (ii)evaluate the efficacy of bioremediation, both biostimulation and bioaugmentation with a lyophilized bacterial consortium (Rhodococcus erythropolis, Pseudomonas sp.), in accelerating hydrocarbon degradation. Metabarcoding analysis revealed a shift in microbial communities, with increased abundance of hydrocarbon-degraders (e.g. Alcanivorax, Thalassospira). Ninety-five hydrocarbonoclastic bacteria were isolated, including key groups from the enriched communities. The lyophilized bacteria added in bioaugmentation, enhanced the abundance of hydrocarbon-degraders over time and were recovered throughout time. Bioremediation treatments favoured biodegradation, achieving over 60 % removal of total petroleum hydrocarbons after 15 days, contrasting with natural attenuation where almost no TPH was removed. This work highlights the potential of bioremediation technologies to accelerate hydrocarbon-degrading activity, for oil spills inside ports.

Seasonal coupling of iron (hydr-) oxides and organic carbon across elevations in Phragmites marshes of Yangtze Estuary

As sea levels rise, coastal tidal wetlands are increasingly threatened by flooding and salt stress, highlighting the importance of iron (Fe) (hydr-) oxides in soil for stabilizing organic carbon (OC). This study focuses on Phragmites australis, common in the Yangtze River Estuary, exploring the interplay between OC and Fe (hydr-) oxides in the rhizosphere of P. australis across various seasons and elevations. It also examines microbial community shifts in the Fe oxidation–reduction cycle. Results show that in the non-growing season (January), Fe (hydr-) oxides and total organic carbon (TOC) levels in the rhizosphere soil of high-tide P. australis are significantly higher than during the growing season (August), with a notable increase in Fe oxide-bound OC (Fe-OC). The content of Fe-OC in tidal wetland soil fluctuates with plant growth stages and elevation. Notably, during the growing season, the Fe-OC content in the rhizosphere of low-tide P. australis is markedly higher than in high-tide areas, reversing in the non-growing season. The presence of P. australis roots is found to significantly enhance the accumulation and coupling of Fe (hydr-) oxides and OC, especially in low-tide areas compared to bare flats. This coupling is affected by the organic matter contributed by roots, microbial metabolism, and redox conditions of the soil. The study also highlights how plant and microbial metabolism regulate the response of rhizosphere Fe-OC across different tidal flat elevations. In low-tide environments during the non-growing season, the prevalence of Fe-reducing bacteria results in decreased Fe-OC content, while in high-tide areas, increased organic matter input boosts complexed Fe-OC formation. Overall, this study emphasizes the significance of plant metabolism in understanding the impact of sea level rise on Fe-OC stores in tidal wetlands, a vital factor for comprehending C cycling mechanisms and assessing C sequestration potential under future climate change scenarios.

Temporal patterns of endophytic microbial heterogeneity across distinct ecological compartments within the Panax ginseng root system following deforestation for cultivation.

Alterations in the microbial community significantly impact the yield and quality of ginseng. Yet, the dynamics of microbial community shifts within the root endophytes of ginseng across varying cultivation periods remain inadequately understood. This study zeroes in on the microbial community variations within the xylem (M), phloem (R), and fibrous roots (X) of ginseng during the fourth (F4) and fifth (F5) years of cultivation, aiming to bridge this research gap. We assessed soil physicochemical properties, enzyme activities, and nine individual saponins, complemented by high-throughput sequencing techniques (16S rDNA and ITS) to determine their profiles. The results showed that cultivation years mainly affected the microbial diversity of endophytic bacteria in ginseng fibrous roots compartment: the ASVs number and α-diversity Chao1 index of bacteria and fungi in F5X compartment with higher cultivation years were significantly higher than those in F4X compartment with lower cultivation years. It is speculated that the changes of fibrous roots bacterial groups may be related to the regulation of amino acid metabolic pathway. Such as D-glutamine and D-glutamate metabolism D-glutamine, cysteine and methionine metabolism regulation. The dominant bacteria in ginseng root are Proteobacteria (relative abundance 52.07-80.35%), Cyanobacteria (1.97-42.52%) and Bacteroidota (1.11-5.08%). Firmicutes (1.28-3.76%). There were two dominant phyla: Ascomycota (60.10-93.71%) and Basidiomycota (2.25-30.57%). Endophytic fungi were more closely related to soil physicochemical properties and enzyme activities. AN, TK, OP, SWC and EC were the main driving factors of endophytic flora of ginseng root. Tetracladium decreased with the increase of cultivation years, and the decrease was more significant in phloem (F4R: 33.36%, F5R: 16.48%). The relative abundance of Bradyrhizobium, Agrobacterium and Bacillus in each ecological niche increased with the increase of cultivation years. The relative abundance of Bradyrhizobium and Agrobacterium in F5X increased by 8.35 and 9.29 times, respectively, and Bacillus in F5M increased by 5.57 times. We found a variety of potential beneficial bacteria and pathogen antagonists related to ginseng biomass and saponins, such as Bradyrhizobium, Agrobacterium, Bacillus and Exophiala, which have good potential for practical application and development.

Bacillus tequilensis influences metabolite production in tomato and restores soil microbial diversity during Fusarium oxysporum infection.

This study evaluates cellular damage, metabolite profiling, and defence-related gene expression in tomato plants and soil microflora during Fusarium wilt disease after treatment with B. tequilensis PBE-1. Histochemical analysis showed that PBE-1 was the primary line of defence through lignin deposition and reduced cell damage. GC-MS revealed that PBE-1 treatment ameliorated stress caused by F. oxysporum infection. PBE-1 also improved transpiration, photosynthesis, and stomatal conductance in tomato. qRT-PCR suggested that the defence-related genes FLS2, SERK, NOS, WRKYT, NHO, SAUR, and MYC2, which spread infection, were highly upregulated during F. oxysporum infection, but either downregulated or expressed normally in PBE-1 + P treated plants. This indicates that the plant not only perceives the bio-control agent as a non-pathogen entity but its presence in normal metabolism and gene expression within the host plant is maintained. The study further corroborated findings that application of PBE-1 does not cause ecological disturbances in the rhizosphere. Activity of soil microflora across four treatments, measured by Average Well Colour Development (AWCD), showed continuous increases from weeks 1 to 4 post-pathogen infection, with distinct substrate usage patterns like tannic and fumaric acids impacting microbial energy source utilization and diversity. Principal Component Analysis (PCA) and diversity indices like McIntosh, Shannon, and Simpson further illustrated significant microbial community shifts over the study period. In conclusion, our findings demonstrate that B. tequilensis PBE-1 is an ideal bio-agent for field application during Fusarium wilt disease management in tomato.

Disentangling the effects of mineral fertiliser N, P and K on microbial biomass, necromass and ionome in soil from the Askov long-term field experiment

Given the increasingly recognised importance of microbial biomass (MB) in soil organic carbon (SOC) sequestration, knowledge of the microbial ionome beyond carbon (C), nitrogen (N) and phosphorus (P) becomes crucial. The microbial ionome could indicate nutritional restrictions related to MB growth and microbial necromass C (MN-C) accumulation. In this study, soils receiving different combinations of mineral N, P and potassium (K) were sampled in the Askov long-term field experiment, Denmark, and analysed for MB elemental composition including N, P, K, magnesium (Mg), manganese (Mn) and zinc (Zn) using fumigation-extraction and ICP-OES. Furthermore, bacterial, archaeal and fungal gene abundance was determined by qPCR as microbial community shifts may relate to microbial ionome shifts. MN-C was determined by amino sugar analysis. MB-C was unaffected by fertiliser treatments and not correlated with MN-C. N fertilisation increased MN-C. N and K additions increased plant-derived SOC, indicating the importance of N for microbial and plant-derived SOC accumulation. Availability of P and K increased MB-P and MB-K, respectively, and reduced the MB-C:P ratio but not MB-C:K. N fertilisation reduced the pH and increased Mn availability which increased MB-Mn and reduced MB-C:Mn. ITS1 gene copies responded positively to P availability. A reduced MB-C:Mn ratio was associated with a relative increase in fungal gene copy abundance. This was linked to an increase in SOC, indicating a positive link between Mn availability, fungal abundance and SOC level, yet this was not reflected in MN-C accumulation, but by the accumulation of plant-derived SOC, possibly due to reduced plant C turnover.

Changes in microbial composition explain the contrasting responses of glucose and lignin decomposition to soil acidification in an alpine grassland

Soil acidification often suppresses microbial growth and activities, resulting in a negative impact on soil organic carbon (C) decomposition. While the detrimental effects of acidification on soil and plant properties have been extensively studied, less attention has been paid on the shifts in soil microbial communities and their influences of the decomposition of organic C with different chemical complexities. Taking advantage of an acid addition experiment in a Tibetan alpine meadow, here we examined the response of soil microbial communities to soil acidification and microbial effect on the decomposition of organic C with different chemical complexities (i.e., glucose and lignin, representing labile and recalcitrant C respectively). We found that soil acidification had no impact on microbial respiration and microbial abundance even though it decreased bacterial diversity significantly. Soil acidification increased the relative abundance of some microbial taxa, like Alphaproteobacteria and Acidobacteriia in bacteria increased by 36 %, 284 %, and Eurotiomycetes, Sordariomycetes and Leotiomycetes in fungi increased by 145 %, 279 % and 12.7-fold, but decreased the relative abundance of Acidimicrobiia by 33 % in highest acid addition treatment. Changes in microbial communities (bacterial and fungal community composition, the diversity of bacterial community and the ratio of fungi to bacteria) are significantly related to the decomposition of glucose and lignin. More specifically, soil acidification decreased the decomposition of glucose but increased the decomposition of lignin, indicating a trade-off between the decomposition of labile and recalcitrant soil organic C under soil acidification. Overall, shifts in microbial communities under soil acidification might be accompanied by an increased ability to break down more recalcitrant C. This trade-off between the decomposition of labile and recalcitrant C may change soil C quality under future acid deposition scenarios.

Unveiling microbial degradation of triclosan: Degradation mechanism, pathways, and catalyzing clean energy

Emerging organic contaminants present in the environment can be biodegraded in anodic biofilms of microbial fuel cells (MFCs). However, there is a notable gap existing in deducing the degradation mechanism, intermediate products, and the microbial communities involved in degradation of broad-spectrum antibiotic such as triclosan (TCS). Herein, the possible degradation of TCS is explored using TCS acclimatized biofilms in MFCs. 95% of 5 mgL−1 TCS are been biodegraded within 84 h with a chemical oxygen demand (COD) reduction of 62% in an acclimatized-MFC (A-MFC). The degradation of TCS resulted in 8 intermediate products including 2,4 -dichlorophenol which gets further mineralized within the system. Concurrently, the 16S rRNA V3–V4 sequencing revealed that there is a large shift in microbial communities after TCS acclimatization and MFC operation. Moreover, 30 dominant bacterial species (relative intensity >1%) are identified in the biofilm in which Sulfuricurvum kujiense, Halomonas phosphatis, Proteiniphilum acetatigens, and Azoarcus indigens significantly contribute to dihydroxylation, ring cleavage and dechlorination of TCS. Additionally, the MFC was able to produce 818 ± 20 mV voltage output with a maximum power density of 766.44 mWm−2. The antibacterial activity tests revealed that the biotoxicity of TCS drastically reduced in the MFC effluent, signifying the non-toxic nature of the degraded products. Hence, this work provides a proof−of−concept strategy for sustainable mitigation of TCS in wastewaters with enhanced bioelectricity generation.

Promoting bioremediation of brewery wastewater, production of bioelectricity and microbial community shift by sludge microbial fuel cells using biochar as anode

Seeking low-cost and eco-friendly electrode catalyst of microbial fuel cell (MFC) reactor has received extensive attention in recent decades. In this study, a sludge MFC was coupled with biochar-modified-anode (BC-300, BC-400, and BC-500) for actual brewery wastewater treatment. The physicochemical properties of biochar largely depended on the pyrolysis temperature, further affecting the removal efficiency of wastewater indicators. BC-400 MFC proved to be efficient for TN and NH4+-N removal, while the maximum removal efficiencies of COD and TP were achieved by BC-500 MFC, reaching respectively 97.14 % and 89.67 %. Biochar could promote the degradation of dissolved organic matter (DOM) in wastewater by increasing the electrochemical performances of MFC. The maximum output voltage of BC-400 MFC reached 410.24 mV, and the maximum electricity generation of 108.05 mW/m2 was also obtained, surpassing the pristine MFC (BCC-MFC) by 4.67 times. High-throughput sequencing results illustrated that the enrichment of electrochemically active bacteria (EAB) and functional bacteria (Longilinea, Denitratisoma, and Pseudomonas) in BC-MFCs, contributed to pollutants degradation and electron transfer. Furthermore, biochar affected directly the electrical conductivity of wastewater, simultaneously changing microbial community composition of MFC anode. Considering both enhanced removal efficiency of pollutants and increased power generation, the results of this study would offer technical reference for the application of biochar as MFC catalyst for brewery wastewater treatment.

The Ability of Vermicompost to Mitigate the Impacts of Salinity Stress on Soil Microbial Community: A Review

Soil salinity is a major challenge in many developing countries, affecting soil fertility and crop productivity. Salinity directly affects the soil microbiome through osmotic pressure and ion toxicity, resulting in diminished microbial biomass and activity. Additionally, indirect repercussions involve reduced organic carbon inputs and aggregate stability, reducing microbial diversity and functions. Salinity induces a microbial community shift toward the abundance of halotolerant and halophile microorganisms. The use of organic amendments is a promising approach. Indeed, the application of vermicompost, with its rich nutrient and organic matter content, proves effective in counteracting the impact of salinity on the soil microbiome by providing available nutrients, decreasing the plasmolysis of cells by reducing the Na+/K+and Na+/Ca2+ratios, improving the soil texture, increasing the microbial diversity, and shifting the soil microbiome toward the abundance of beneficial soil microbiota. Despite these positive effects, carefully considering the initial EC of both soil and vermicompost and the applied quantity is crucial to ensuring maximum benefits. Overall, vermicompost holds considerable potential as a sustainable management strategy to mitigate the impact of salinity on soil microbiome, promoting overall soil health and enhancing crop production.

Response of bacterial communities, enzyme activities and dynamic changes of soil organic nitrogen fractions to six-year different application levels of biochar retention in Northeast China

Composition and availability of soil organic nitrogen play a key role in soil N retention and supply. The application of traditional chemical fertilizers can improve soil production and crop yields. However, it also leads to low N utilization efficiency and soil solidification. Previous studies have shown that fertilizers added with biochar can improve soil fertility and facilitate soil nutrient transformation by regulating soil biological indicators. However, whether biochar used with fertilizers can promote nutrient cycling in the long term, which remains to be tested. Therefore, this study aims to explore the long-term effects of biochar with different levels used with fertilizers on soil fertility, N supply potential of organic N, and microbial communities, thus, providing a theoretical reference for the rational management of biochar applications. In this study, a field experiment was carried out from 2013 to 2018 assess dynamic changes in organic N fractions and diversity and richness of microbial communities under the impacts of chemical fertilizers combined with different levels of biochar. Biochar with no amendment (CK), biochar with 15.75 t ha−1 (BC1), biochar with 31.5 t ha−1 (BC2), and biochar with 47.25 t ha−1 (BC3) are four biochar levels that were tested in this study. The results show that compared with CK, those other three biochar levels can increase soil organic matter, C/N, and pH values. Acid-hydrolysable N (AHN) makes a major contribution to organic N in soil. Biochar retention for six years has significantly affected AHN levels, as well as its four fractions, namely, amino acid N (AAN), acid-hydrolysable ammonium N (AN), amino sugar N (ASN), and hydrolysable unknown N (HUN). Some vital biological characteristics, with which each AHN fraction is primarily regulated, can be altered with the application of biochar. That is, AAN is mainly controlled by enriched Verrucomicrobia, Cyanobacteria, Glucosylbacteria, and Nitrospira, and reduced soil urease, while AN is mainly controlled by enriched Verrucomicrobia, Bacteroidetes, Gemmatimonadetes, Acidobacteria, and Proteobacteria. ASN is regulated by enriched Acidobacteria and depleted soil protease, while HUN is regulated by Gemmatimonadetes and enriched soil nitrate reductase. It has been found that microbial and soil enzyme activities are involved in N cycle processes, indicating that the formation of AHN fractions is closely associated with biochar-induced specific microbial and enzyme activities. This study has provided new insights into the influences of biochar with different levels on distribution of soil organic N fractions, and shifts in soil enzyme activities and microbial communities.

Microorganisms uniquely capture and predict stony coral tissue loss disease and hurricane disturbance impacts on US Virgin Island reefs.

Coral reef ecosystems are now commonly affected by major climate and disease disturbances. Disturbance impacts are typically recorded using reef benthic cover, but this may be less reflective of other ecosystem processes. To explore the potential for reef water-based disturbance indicators, we conducted a 7-year time series on US Virgin Island reefs where we examined benthic cover and reef water nutrients and microorganisms from 2016 to 2022, which included two major disturbances: hurricanes Irma and Maria in 2017 and the stony coral tissue loss disease outbreak starting in 2020. The disease outbreak coincided with the largest changes in the benthic habitat, with increases in the percent cover of turf algae and Ramicrusta, an invasive alga. While sampling timepoint contributed most to changes in reef water nutrient composition and microbial community beta diversity, both disturbances led to increases in ammonium concentration, a mechanism likely contributing to observed microbial community shifts. We identified 10 microbial taxa that were sensitive and predictive of increasing ammonium concentration. This included the decline of the oligotrophic and photoautotrophic Prochlorococcus and the enrichment of heterotrophic taxa. As disturbances impact reefs, the changing nutrient and microbial regimes may foster a type of microbialization, a process that hastens reef degradation.

Soil warming-induced reduction in water content enhanced methane uptake at different soil depths in a subtropical forest

Global warming can significantly impact soil CH4 uptake in subtropical forests due to changes in soil moisture, temperature sensitivity of methane-oxidizing bacteria (MOB), and shifts in microbial communities. However, the specific effects of climate warming and the underlying mechanisms on soil CH4 uptake at different soil depths remain poorly understood. To address this knowledge gap, we conducted a soil warming experiment (+4 °C) in a natural forest. From August 2020 to October 2021, we measured soil temperature, soil moisture, and CH4 uptake rates at four different soil depths: 0–10 cm, 10–20 cm, 20–40 cm, and 40–60 cm. Additionally, we assessed the soil MOB community structure and pmoA gene (with qPCR) at the 0–10 and 10–20 cm depths. Our findings revealed that warming significantly enhanced soil net CH4 uptake rate by 12.28 %, 29.51 %, and 61.05 % in the 0–10, 20–40, and 40–60 cm soil layers, respectively. The warming also led to reduced soil moisture levels, with more pronounced reductions observed at the 20–40 cm depth compared to the 0–20 cm depth. At the 0–10 cm depth, warming increased the relative abundance of upland soil cluster α (a type of MOB) and decreased the relative abundance of Methylocystis, but it did not significantly increase the pmoA gene copies. Our structural equation model analysis indicated that warming directly regulated soil CH4 uptake rate through the decrease in soil moisture, rather than through changes in the pmoA gene and MOB community structure at the 0–20 cm depth. In summary, our results demonstrate that warming enhances soil CH4 uptake at different depths, with soil moisture playing a crucial role in this process. Under warming conditions, the drier soil pores allow for better CH4 penetration, thereby promoting more efficient activity of MOB.