Microbial Functional Genes Research Articles

Enhanced remediation of chlorpyrifos-contaminated soil by immobilized strain Bacillus H27

Chlorpyrifos is a pesticide widely used in agricultural production with a relatively long residual half-life in soil. Addressing the problem of residual chlorpyrifos is of universal concern. In this study, rice hull biochar was used as an immobilized carrier to prepare the immobilized strain H27 for the remediation of chlorpyrifos-contamination soil. Soil microorganisms after remediation were investigated by ecotoxicological methods. The immobilized strain H27 had the highest removal rate of chlorpyrifos when 10% bacterial solution was added to the liquid medium containing 0.075-0.109 mm diameter biochar cultured for 22 hr. This study on the removal of chlorpyrifos by immobilized strain H27 showed that the initial concentration of chlorpyrifos in solution was 25 mg/L, and the removal rate reached 97.4% after 7 days of culture. In the soil, the removal rate of the immobilized bacteria group increased throughout the experiment, which was significantly higher than that of the free bacteria and biochar treatment groups. The Biolog-ECO test, T-RFLP and RT-RCR were used to study the effects of the soil microbial community and nitrogen cycling functional genes during chlorpyrifos degradation. It was found that ICP group had the highest diversity index among the four treatment groups. The microflora of segment containing 114 bp was the dominant bacterial community, and the dominant microflora of the immobilized bacteria group was more evenly distributed. The influence of each treatment group on ammonia-oxidizing bacteria (AOB) was greater than on ammonia-oxidizing archaea (AOA). This study offers a sound scientific basis for the practical application of immobilized bacteria to reduce residual soil pesticides.

Relationships between nitrogen-specific genes and soil potentials are more complex than single linear ones

Linkages between soil potentials and microbial functional genes are central in microbial ecology, though conflicting results have been obtained. Here, we investigated such linkages for log-transformed abundances of nitrogen (N) genes from grassland soils. The soil nitrification potential increased with rising A-amoA abundance only after it reaching 8.49 × e10 copy numbers g−1 soil, while the denitrification potential was positively correlated with narG and nirS after 8.44 × e10 and 8.12 × e10 copy numbers g−1 soil, respectively. Moreover, nitrification potential increased with rising ratio of A-amoA/B-amoA more strongly with a higher R2 after a threshold of 5.94, indicating that A-amoA controlled corresponding potential when it was abundant enough to overwhelm B-amoA. Our evaluation revealed the complexity between specific N genes and soil potentials, which were far from single linear relationships and abundant enough genes are necessary to correlate positively with corresponding functional potentials.

Role of microplastics in microbial community structure and functions in urban soils

Evidence from the laboratory suggests that microplastics (MPs) can harm soil microorganisms, affecting the structures and functions of microbial communities. The impact of soil MPs on microbes in actual urban environments with high human activity levels, however, has not been well reported. To investigate the MP effect on urban soil microorganisms under complex scenarios, we analyzed 42 soil samples from standardized plots of 7 urban functional zones. We report that urban green spaces are important for studying microbial diversity in the study area, and they also contribute to the global homogenization of soil microbes and genes. Bacterial communities in soils enriched with various MPs showed greater differences in OTUs than fungi. Compared to low-MP soils, most ARGs and nutrient cycling genes had similar or slightly lower abundances in soils with high levels of MPs. The coupling of pollutant factors with MPs as independent variables had significant explanatory power for both positive and negative correlations in PLS-PM analysis. Specifically, PET and PP MPs explained 3.54% and 6.03%, respectively, of the microbial community and functional genes. This study fills knowledge gaps on the effects of MPs on urban soil microbial communities in real environments, facilitating better management of urban green spaces.

Stimulation of primed carbon under climate change corresponds with phosphorus mineralization in the rhizosphere of soybean

Elevated CO2 and temperature likely alter photosynthetic carbon inputs to soils, which may stimulate soil microbial activity to accelerate the decomposition of soil organic carbon (SOC), liberating more phosphorus (P) into the soil solution. However, this hypothesis on the association of SOC decomposition and P transformation in the plant rhizosphere requires robust soil biochemical evidence, which is critical to nutrient management for the mitigation of soil quality against climate change. This study investigated the microbial functional genes relevant to P mineralization together with priming processes of SOC in the rhizosphere of soybean grown under climate change. Soybean plants were grown under elevated CO2 (eCO2, 700 ppm) combined with warming (+ 2 °C above ambient temperature) in open-top chambers. Photosynthetic carbon flow in the plant–soil continuum was traced with 13CO2 labeling. The eCO2 plus warming treatment increased the primed carbon (C) by 43 % but decreased the NaHCO3-extratable organic P by 33 %. Furthermore, NaHCO3-Po was negatively correlated with phosphatase activity and microbial biomass C. Elevated CO2 increased the abundances of C degradation genes, such as abfA and ManB, and P mineralization genes, such as gcd, phoC and phnK. The results suggested that increased photosynthetic carbon inputs to the rhizosphere of plants under eCO2 plus warming stimulated the microbial population and metabolic functions of both SOC and organic P mineralization. There is a positive relationship between the rhizosphere priming effect and P mineralization. The response of microorganisms to plant-C flow is decisive for coupled C and P cycles, which are likely accelerated under climate change.

Macrofungi promote SOC decomposition and weaken sequestration by modulating soil microbial function in temperate steppe

Soil organic carbon (SOC) sequestration is a key grassland ecosystem function, and the magnitude of SOC reservoirs depends on microbial involvement, especially that of fungi. Mycelia developed by macrofungi potentially influence carbon (C) fixation and decomposition; however, the mechanisms underlying their effects on SOC storage in grassland ecosystems remain poorly understood. The fairy rings formed by macrofungi in grasslands are natural platform for exploring macrofungal effects on SOC. In this study, we collected topsoil (0–10 cm) from four different fairy ring zones in a temperate steppe to reveal the macrofungal effects on SOC fractions, including particulate organic carbon (POC) and mineral-associated organic carbon (MAOC), and the SOC storage microbial mechanism using metagenomic sequencing technology. Both POC and MAOC decreased after macrofungal passage, resulting in a 7.37 % reduction in SOC. Macrofungal presence reduced microbial biomass carbon (MBC), but significantly enhanced the β-1,4-glucosidase (BG) activity, which increased dissolved organic carbon (DOC). In addition, the abundance of copiotrophs (Proteobacteria and Bacteroidetes) with lower C metabolic rates increased, and that of oligotrophs (Actinobacteria, Acidobacteria, Chloroflexi, and Verrucomicrobia) with higher substrate utilization efficiency decreased in the presence of macrofungi. This may further promote SOC decomposition. Correspondingly, there was a lower abundance of C-fixation genes but more C-degradation genes (especially hemicellulosic degradation genes) during macrofungal passage. Our results indicate that the presence of macrofungi can modulate the soil microbial community and functional genes to reduce SOC storage by inhibiting microbial C sequestration while promoting C decomposition in grassland ecosystems. These findings refine our mechanistic understanding of SOC persistence through the interactions between macrofungi and other microbes.

Effects of straw and plastic film mulching on microbial functional genes involved in soil nitrogen cycling.

Microorganisms regulate soil nitrogen (N) cycling in cropping systems. However, how soil microbial functional genes involved in soil N cycling respond to mulching practices is not well known. We collected soil samples from a spring maize field mulched with crop straw (SM) and plastic film (FM) for 10-year and with no mulching (CK) in the Loess Plateau. Microbial functional genes involved in soil N cycling were quantified using metagenomic sequencing. We collected soil samples from a spring maize field mulched with crop straw (SM) and plastic film (FM) for 10-year and with no mulching (CK) in the Loess Plateau. Microbial functional genes involved in soil N cycling were quantified using metagenomic sequencing. Compared to that in CK, the total abundance of genes involved in soil N cycling increased in SM but had no significant changes in FM. Specifically, SM increased the abundances of functional genes that involved in dissimilatory nitrate reduction to ammonium (nirB, napA, and nrfA), while FM decreased the abundances of functional genes that involved in ammonification (ureC and ureA) in comparison with CK. Other genes involved in assimilatory nitrate reduction, denitrification, and ammonia assimilation, however, were not significantly changed with mulching practices. The nirB and napA were derived from Proteobacteria (mainly Sorangium), and the ureC was derived from Actinobacteria (mainly Streptomyces). Mental test showed that the abundance of functional genes that involved in dissimilatory nitrate reduction was positively correlated with the contents of soil microbial biomass N, potential N mineralization, particulate organic N, and C fractions, while ammonification related gene abundance was positively correlated with soil pH, microbial biomass C and N, and mineral N contents. Overall, this study showed that SM could improve soil N availability and promote the soil N cycling by increasing the abundance of functional genes that involved in DNRA, while FM reduced the abundance of functional genes that involved in ammonification and inhibited soil N cycling.

Unlocking the potential of resuscitation-promoting factor for enhancing anaerobic microbial dechlorination of polychlorinated biphenyls

Microbial dechlorination of polychlorinated biphenyls (PCBs) is limited by the slow growth rate and low activity of dechlorinators. Resuscitation promoting factor (Rpf) of Micrococcus luteus, has been demonstrated to accelerate the enrichment of highly active PCB-dechlorinating cultures. However, it remains unclear whether the addition of Rpf can further improve the dechlorination performance of anaerobic dechlorination cultures. In this study, the effect of Rpf on the performance of TG4, an enriched PCB-dechlorinating culture obtained by Rpf amendment, for reductive dechlorination of four typical PCB congeners (PCBs 101, 118, 138, 180) was evaluated. The results indicated that Rpf significantly enhanced the dechlorination of the four PCB congeners, with residual mole percentages of PCBs 101, 118, 138 and 180 in Rpf-amended cultures being 16.2–29.31 %, 13.3–20.1 %, 11.9–14.4 % and 9.4–17.3 % lower than those in the corresponding cultures without Rpf amendment after 18 days of incubation. Different models were identified as appropriate for elucidating the dechlorination kinetics of distinct PCB congeners, and it was observed that the dechlorination rate constant is significantly influenced by the PCB concentration. The supplementing Rpf did not obviously change dechlorination metabolites, and the removal of chlorines occurred mainly at para- and meta- positions. Analysis of microbial community and functional gene abundance suggested that Rpf-amended cultures exhibited a significant enrichment of Dehalococcoides, Dehalogenimonas and Desulfitobacterium, as well as non-dechlorinators belonging to Desulfobacterota and Bacteroidetes. These findings highlight the potential of Rpf as an effective additive for enhancing PCB dechlorination, providing new insights into the survival of functional microorganisms involved in anaerobic reductive dechlorination.

Revisiting the relationships between soil nitrous oxide emissions and microbial functional gene abundances.

A conceptual framework proposes that soil N2 O emissions are more likely related to microbial functional gene abundances based on laboratory experiments than in-situ observations. This framework has largely contributed to reconciling the disputation on linking soil N2 O emissions with functional gene abundances, but the direct evidence is lacking. Wei et al. (2023) provided new evidence to support this framework, showing that O2 dynamics were a better predictor of in-situ soil N2 O emissions than were functional gene abundances. Before the observations can inform N2 O modeling and support sustainable nitrogen management, however, some additional efforts are needed to revisit the relationships between in-situ soil N2 O emissions and functional gene abundances.

Coal gangue-based magnetic porous material for simultaneous remediation of arsenic and cadmium in contaminated soils: Performance and mechanisms

Remediation of arsenic (As) and cadmium (Cd) co-contaminated soil is a challenge in environmental remediation. In this study, coal gangue-based magnetic porous material (MPCG) was designed for simultaneous immobilization of As and Cd in contaminated soil. After the incubation experiment, the effects of CG and MPCG on the availability and fractions of As and Cd and the related microbial functional genes were analyzed to explore the potential remediation mechanisms of MPCG for As and Cd in contaminated soil. The results showed that the stabilization effect of MPCG on As and Cd was significantly higher than that of coal gangue. It reduced the available As and Cd by 17.94–29.81% and 14.22–30.41%, respectively, and transformed unstable As/Cd to stable. The remediation mechanisms of MPCG on As included adsorption, oxidation, complexation and precipitation/co-precipitation. Meanwhile, the remediation mechanisms of MPCG for Cd included adsorption, ion exchange, complexation and precipitation. In addition, MPCG increases the abundance of sulfate-reducing bacteria (dsrA) by 43.39–381.28%, which can promote sulfate reduction. The sulfide can precipitate with As and Cd to reduce the availability of As and Cd in soil. Thus, MPCG is a promising amendment for achieving the remediation of As and Cd co-contaminated soil.

The Nitrogen Cycling Key Functional Genes and Related Microbial Bacterial Community α−Diversity Is Determined by Crop Rotation Plans in the Loess Plateau

Soil nitrogen cycling microbial communities and functional gene α−diversity indicate soil nitrogen cycling ecological functions and potentials. Crop rotation plans affect soil nitrogen fractions and these indicators. We sequenced soil samples from four crop rotation plans (fallow, winter wheat monoculture, pea-winter wheat-winter wheat-millet rotation, and corn-wheat-wheat-millet rotation) in a long-term field experiment. We examined how microbial communities and functional gene α−diversity changed with soil nitrogen fractions and how nitrogen fractions regulated them. Planting crops increased the abundance and richness of nitrogen cycling key functional genes and bacterial communities compared with fallow. The abundance and richness correlated positively with nitrogen fractions, while Shannon index did not. The abundance increased with soil total nitrogen (STN) and potential nitrogen mineralization (PNM), while Shannon index showed that nitrogen cycling key functional genes increased and then decreased with increasing STN and PON. Introducing legumes into the rotation improved the α−diversity of nitrogen cycling key functional genes. These results can guide sustainable agriculture in the Loess Plateau and clarify the relationship between nitrogen fractions and nitrogen cycling key functional genes.

Mill dams impact microbiome structure and depth distribution in riparian sediments.

Damming has substantially fragmented and altered riverine ecosystems worldwide. Dams slow down streamflows, raise stream and groundwater levels, create anoxic or hypoxic hyporheic and riparian environments and result in deposition of fine sediments above dams. These sediments represent a good opportunity to study human legacies altering soil environments, for which we lack knowledge on microbial structure, depth distribution, and ecological function. Here, we compared high throughput sequencing of bacterial/ archaeal and fungal community structure (diversity and composition) and functional genes (i.e., nitrification and denitrification) at different depths (ranging from 0 to 4 m) in riparian sediments above breached and existing milldams in the Mid-Atlantic United States. We found significant location- and depth-dependent changes in microbial community structure. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Chloroflexi, Acidobacteria, Planctomycetes, Thaumarchaeota, and Verrucomicrobia were the major prokaryotic components while Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, Mucoromycota, and Rozellomycota dominated fungal sequences retrieved from sediment samples. Ammonia oxidizing genes (amoA for AOA) were higher at the sediment surface but decreased sharply with depth. Besides top layers, denitrifying genes (nosZ) were also present at depth, indicating a higher denitrification potential in the deeper layers. However, these results contrasted with in situ denitrification enzyme assay (DEA) measurements, suggesting the presence of dormant microbes and/or other nitrogen processes in deep sediments that compete with denitrification. In addition to enhanced depth stratification, our results also highlighted that dam removal increased species richness, microbial diversity, and nitrification. Lateral and vertical spatial distributions of soil microbiomes (both prokaryotes and fungi) suggest that not only sediment stratification but also concurrent watershed conditions are important in explaining the depth profiles of microbial communities and functional genes in dammed rivers. The results also provide valuable information and guidance to stakeholders and restoration projects.

Linking soil phosphorus fractions to associated microbial functional profiles under crop rotation on the Loess Plateau of China

Crop rotation plays an essential role in maintaining soil fertility and is meaningful to soil health and sustainable agricultural management. However, the impact of crop rotational regimes on the soil phosphorus (P) fractions and associated phosphorus cycling (P-cycling) profiles driven by microbial communities are not well elucidated. Hence, we used metagenomics to comprehensively investigate the variations in soil microbial P-cycling functional genes and representative processes, as well their regulations for soil P fractions among distinct crop rotational regimes and complexity. Most soil properties, particularly P fractions, were significantly greater in corn rotations than other crop rotations. The composition of P-cycling functional genes and microbial communities was also distinctly clustered in accordance with crop rotational regimes to varying degrees. The potential of representative P-cycling processes was all significantly higher in the complex rotation. Notably, the key functional genes including phoD, ppx, pstB, ugpA were differently screened from each P-cycling process and assembled toward the middle of their networks. Furthermore, soil potential carbon mineralization as a dominant property regulated several P-cycling processes and was intimately associated with the key P-cycling functional genes. Crop rotational complexity and the P-uptake and transport process had profoundly total effects on soil P fractions. Overall, this study provides a deep insight into soil microbial P-cycling functional profiles for developing sustainable soil P management practices at crop rotational agroecosystems.

Response of rare and abundant rhizosphere microbial communities to inoculated rhizobium in cadmium-contaminated soil phytoremediation

Soil microorganisms play an important role in maintaining ecosystem balance and exerting ecological functions. The taxonomic and functional changes in rare and abundant communities during in bioremediation of cadmium-contaminated soils and their contributions to the remediation of ecosystem functions remain elusive despite the significance of rare and abundant microbial taxa in maintaining soil ecological function. Mesorhizobiumloti HZ76-inoculated seedlings of the Robinia pseudoacacia were used to create a symbiotic system. The effects of rhizobium inoculation on rare and abundant rhizosphere microbial populations were investigated in pot experiments. Despite having minimal effects on the α-diversity of rare and abundant microbial communities, inoculation altered microbial community composition and functional gene abundance. For example, abundant phyla such as Proteobacteria were enriched following inoculation, whereas rare phyla such as Ascomycota were depleted. After inoculation, the abundance of nifH gene increased, while the abundance of amoA, amoB, nirS, nirK and nosZ gene decreased. Rare bacterial populations were more susceptible to the inoculated rhizobium's environmental alterations. In rare communities compared to abundance communities, the α-diversity was higher. Stochastic processes predominated in the communities of uncommon and abundant microorganisms. Furthermore, keystone taxa, particularly rare bacterial taxa (Gemmatimonadaceae and Saprospiraceae) and rare fungal taxa (Ascomycota), more mediates nitrogen cycle processes and is directly associated to the abundance of nitrogen functional genes. Together, our findings demonstrate the different ways that rare and abundant microbial species react to rhizobia inoculation and their connections to the nitrogen cycle.

Cadaverine and putrescine exposure influence carbon and nitrogen cycling genes in water and sediment of the Yellow River

The response patterns of microbial functional genes involved in biogeochemical cycles to cadaver decay is a central topic of recent environmental sciences. However, the response mechanisms and pathways of the functional genes associated with the carbon (C) and nitrogen (N) cycling to cadaveric substances such as cadaverine and putrescine remain unclear. This study explored the variation of functional genes associated with C fixation, C degradation and N cycling and their influencing factors under cadaverine, putrescine and mixed treatments. Our results showed only putrescine significantly increased the alpha diversity of C fixation genes, while reducing the alpha diversity of N cycling genes in sediment. For the C cycling, the mixed treatment significantly decreased the total abundance of reductive acetyl-CoA pathway genes (i.e., acsB and acsE) and lig gene linked to lignin degradation in water, while only significantly increasing the hydroxypropionate-hydroxybutylate cycle (i.e., accA) gene abundance in sediment. For the N cycling, mixed treatment significantly decreased the abundance of the nitrification (i.e., amoB), denitrification (i.e., nirS3) genes in water and the assimilation pathway gene (i.e., gdhA) in sediment. Environmental factors (i.e., total carbon and total nitrogen) were all negatively associated with the genes of C and N cycling. Therefore, cadaverine and putrescine exposure may inhibit the pathway in C fixation and N cycling, while promoting C degradation. These findings can offer some new insight for the management of amine pollution caused by animal cadavers.

Performance changes in the anammox process under the stress of rare-earth element Ce(III) and the evolution of microbial community and functional genes

The high Ce(III) content in ionic rare-earth tailings wastewater has hindered the application of anammox process in this field. Here, the effect of Ce(III) on the performance of anammox processes was investigated, and the evolution of microbial communities and functional genes was explored using metagenomic sequencing. The results showed that the reactor nitrogen removal rate decreased when the Ce(III) concentration reached 25 mg/L, although ammonia nitrogen removal (92.31%) and nitrogen removal efficiency (81.33%) remained at a high level; however, both showed a significant decreasing trend. The relative abundance of anammox bacteria increased continuously from P1–P5, reaching 48.81%, whereas the relative abundance of Candidatus jettenia reached 33.71% at P5, which surpassed that of Candidatus brocadia as the most abundant anammox bacteria, and further analysis of functional genes and metabolic pathways revealed that Candidatus brocadia was richer in biochemical metabolic genes, whereas Candidatus jettenia had richer efflux genes.

Effects of extreme drought on soil microbial functional genes involved in carbon and nitrogen cycling in alpine peatland

Diverse microorganisms drive biogeochemical cycles and consequently influence ecosystem-level processes in alpine peatlands, which are vulnerable to extreme drought induced by climate change. However, there are few reports about the effects of extreme drought on microbial function. Here we identify microbial functional genes associated with carbon and nitrogen metabolisms of extreme drought experiments that occurred at different periods of plant growth, the results show that early extreme drought reduces the abundance of functional genes involved in the decomposition of starch and cellulose; midterm extreme drought increases the abundance of lignin decomposition functional genes; late extreme drought reduces the hemicellulose but increases cellulose decomposition functional genes. In the carbon fixation pathway, extreme drought mainly changes the abundance of functional genes involved in the reductive citrate cycle process, the 3-hydroxy propionate bi-cycle, the dicarboxylate-hydroxybutyrate cycle and the incomplete reductive citrate cycle. Among the nitrogen cycling functional genes, amoA involved in oxidizing ammonia to hydroxylamine significantly increases under early extreme drought; midterm extreme drought reduces nrtC and nifD genes, which participate in nitrate assimilation and nitrogen fixation, respectively; late extreme drought significantly increases hcp genes involved in ammonification. pH and TN had the largest effects on the carbon degradation, fixation and nitrogen cycling functional genes. The composition of microbial community structures involved in carbon fixation differed between treatments in early extreme drought. There is a good linear fit between the diversity of gene abundance and corresponding microbial communities in the reductive citrate cycle, hydroxy propionate-hydroxybutyrate cycle, dicarboxylate-hydroxybutyrate cycle and nitrogen cycling, which suggests that the functional genes and community composition of microorganisms involved in these processes are consistent in response to extreme drought. This study provides new insights into the adaptability and response characteristics of microbial communities and functional genes in plateau peatland ecosystems to extreme drought events.

Metagenomic analysis reveals the efficient digestion mechanism of corn stover in Angus bull rumen: Microbial community succession, CAZyme composition and functional gene expression

Ruminant rumen is a biological fermentation system that can efficiently degrade lignocellulosic biomass. The knowledge about mechanisms of efficient lignocellulose degradation with rumen microorganisms is still limited. In this study, composition and succession of bacteria and fungi, carbohydrate-active enzymes (CAZymes), and functional genes involved in hydrolysis and acidogenesis were revealed during fermentation in Angus bull rumen via metagenomic sequencing. Results showed that degradation efficiency of hemicellulose and cellulose reached 61.2% and 50.4% at 72 h fermentation, respectively. Main bacterial genera were composed of Prevotella, Butyrivibrio, Ruminococcus, Eubacterium, and Fibrobacter, and main fungal genera were composed of Piromyces, Neocallimastix, Anaeromyces, Aspergillus, and Orpinomyces. Principal coordinates analysis indicated that community structure of bacteria and fungi dynamically changed during 72 h fermentation. Bacterial networks with higher complexity had stronger stability than fungal networks. Most CAZyme families showed a significant decrease trend after 48 h fermentation. Functional genes related to hydrolysis decreased at 72 h, while functional genes involved in acidogenesis did not change significantly. These findings provide a in-depth understanding of mechanisms of lignocellulose degradation in Angus bull rumen, and may guide the construction and enrichment of rumen microorganisms in anaerobic fermentation of waste biomass.

The impacts of ocean acidification, warming and their interactive effects on coral prokaryotic symbionts

BackgroundReef-building corals, the foundation of tropical coral reefs, are vulnerable to climate change e.g. ocean acidification and elevated seawater temperature. Coral microbiome plays a key role in host acclimatization and maintenance of the coral holobiont’s homeostasis under different environmental conditions, however, the response patterns of coral prokaryotic symbionts to ocean acidification and/or warming are rarely known at the metatranscriptional level, particularly the knowledge of interactive and persistent effects is limited. Using branching Acropora valida and massive Galaxea fascicularis as models in a lab system simulating extreme ocean acidification (pH 7.7) and/or warming (32 °C) in the future, we investigated the changes of in situ active prokaryotic symbionts community and gene expression of corals under/after (6/9 d) acidification (A), warming (H) and acidification–warming (AH) by metatranscriptome analysis with pH8.1, 26 °C as the control.ResultsA, H and AH increased the relative abundance of in situ active pathogenic bacteria. Differentially expressed genes (DEGs) involved in virulence, stress resistance, and heat shock proteins were up-regulated. Many DEGs involved in photosynthesis, carbon dioxide fixation, amino acids, cofactors and vitamins, auxin synthesis were down-regulated. A broad array of new DEGs involved in carbohydrate metabolism and energy production emerged after the stress treatment. Different response patterns of prokaryotic symbionts of massive G. fascicularis and branching A. valida were suggested, as well as the interactive effects of combined AH and persistent effects.ConclusionsThe metatranscriptome-based study indicates that acidification and/or warming might change coral’s in situ active prokaryotic microbial diversity and functional gene expression towards more pathogenic and destabilized coral-microbes symbioses, particularly combined acidification and warming show interactive effects. These findings will aid in comprehension of the coral holobiont’s ability for acclimatization under future climate change.

Simultaneous Removal of Nitrate and Phosphate in a Pyrrhotite and Sulfur-Circulating Packed Bed Reactor

A pyrrhotite and sulfur-circulating packed bed reactor (PS-CPBR) was constructed to study the removal process and mechanism of NO3−-N and PO43−-P with different electron donors. The results showed that the NO3−-N and PO43−-P removal performance of mixed electron donors (pyrrhotite and sulfur) was superior to the single electron donor (pyrrhotite). The optimum conditions of NO3−-N and PO43−-P removal in the PS-CPBR were a hydraulic retention time (HRT) of 12 h and a C/N of 0, and the average removal efficiency was 100% and 86.39%. The sulfur in mixed electron donors was able to promote the dissolution of pyrrhotite and the formation of polysulfide to increase the effectiveness of electron donors, promoting the removal of NO3−-N, while the PO43−-P was removed in the form of FePO4 precipitation. Microbial and functional gene analyses demonstrated that different electron donors were able to influence the abundance of microbial communities and denitrification functional genes. Meanwhile, mixed electron donors were able to increase the protein content of biofilms and reduce the resistance of electron transfer between microorganisms and electrons.

Microorganisms in coastal wetland sediments: a review on microbial community structure, functional gene, and environmental potential.

Coastal wetlands (CW) are the junction of the terrestrial and marine ecosystems and have special ecological compositions and functions, which are important for maintaining biogeochemical cycles. Microorganisms inhabiting in sediments play key roles in the material cycle of CW. Due to the variable environment of CW and the fact that most CW are affected by human activities and climate change, CW are severely degraded. In-depth understanding of the community structure, function, and environmental potential of microorganisms in CW sediments is essential for wetland restoration and function enhancement. Therefore, this paper summarizes microbial community structure and its influencing factors, discusses the change patterns of microbial functional genes, reveals the potential environmental functions of microorganisms, and further proposes future prospects about CW studies. These results provide some important references for promoting the application of microorganisms in material cycling and pollution remediation of CW.