Abundance Of Functional Genes Research Articles

Bioconversion of citrus waste by long-term DMSO-cryopreserved rumen fluid to volatile fatty acids and biogas is feasible: A microbiome perspective

Preserving rumen fluid as the inoculum for anaerobic digestion of food waste is necessary when access to animal donors or slaughterhouses is limited. This study aims to compare two preservation methods relative to fresh ruminal inoculum: (1) cryoprotected with 5% dimethyl sulfoxide (DMSO) and stored at −20 °C and (2) frozen at −20 °C, both for 6 months. The fermentation activity of different inoculum was evaluated by rumen-based in vitro anaerobic fermentation tests (volatile fatty acids, biomass digestibility, and gas production). Citrus pomace was used as the substrate during a 96-h fermentation. The maximum volatile fatty acids, methane production, and citrus pomace digestibility from fresh rumen fluid were not significantly different from rumen fluid preserved with DMSO. Metagenome analysis revealed a significant difference in the rumen microbial composition and functions between fresh rumen fluid and frozen inoculum without DMSO. Storage of rumen fluid using −20 °C with DMSO demonstrated the less difference compared with fresh rumen fluid in microbial alpha diversity and taxa composition. The hierarchical clustering tree of CAZymes showed that DMSO cryoprotected fluid was clustered much closer to the fresh rumen fluid, showing more similarity in CAZyme profiles than frozen rumen fluid. The abundance of functional genes associated with carbohydrate metabolism and methane metabolism did not differ between fresh rumen fluid and the DMSO–20 °C, whereas the abundance of key functional genes significantly decreased in frozen rumen fluid. These findings suggest that using rumen liquid preserved using DMSO at −20 °C for 180 days is a feasible alternative to fresh rumen fluid. This would reduce the need for laboratories to maintain animal donors and/or reduce the frequency of collecting rumen fluid from slaughterhouses.

Landscape differentiation of soil bacteria and bacteria-soil-vegetation interactions in desert-oasis ecosystems

Desertification control and oasis management are of strategic importance for the protection of ecological security and the achievement of sustainable development in arid regions. However, the role of soil microorganisms in desertification and oasification has been historically overlooked, especially for the influence of microbial communities on landscape change and the stability of soil-vegetation system in desert-oasis ecosystems. Here, using an environmental sampling approach combined with functional annotation, the landscape differentiation of soil bacterial diversity, community structure and functional traits, as well as the bacteria-soil-vegetation interactions were investigated in desert, oasis and desert-oasis ecotone habitats. The results showed that soil bacterial diversity increased significantly from desert, ecotone to oasis, and the highest spatial differentiation of bacterial diversity was observed in desert. The simplest and unique bacterial composition was detected in desert, which was dominant by Arthrobacter, Streptomyces, Burkholderia, etc. However, the phyla Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, and the genus Candidatus_Nitrososphaera were the crucial biomarkers for distinguishing the composition differences across different landscapes. In terms of bacterial composition shift, it was far more challenging to go from ecotone to oasis than from desert to ecotone. Meanwhile, the most stable functional network was exhibited in oasis, while the simplest network was detected in ecotone rather than in desert. Relatively high soil moisture, total nitrogen, organic carbon, total phosphorus, and silt and clay proportions played decisive roles in improving microbial diversity, community structure and functional service, which would enhance the stability and diversity of desert-oasis ecosystems. Furthermore, increase in the relative abundances of functional genes, which were related to metabolism, environmental information processing, and organismal systems, may be harmful to nitrogen cycling and vegetation growth. These results conclude that the landscape differentiation of soil bacteria in desert, ecotone and oasis identifies the central role of bacterial interactions in ecosystem processes and highlights the importance of landscape stability control, forming a novel perspective of microbial behaviour in controlling landscape stability in desert-oasis ecosystems.

Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome.

Soil and plant-associated protistan communities play a key role in shaping bacterial and fungal communities, primarily through their function as top-down predators. However, our understanding of how pathogen invasion influences these protistan communities and their relationships with bacterial and fungal communities remains limited. Here, we studied the protistan communities along the soil-plant continuum of healthy chilli peppers and those affected by Fusarium wilt disease (FWD), and integrated bacterial and fungal community data from our previous research. Our research showed that FWD was associated with a significant enrichment of phagotrophic protists in roots, and also increased the proportion and connectivity of these protists (especially Cercozoa and Ciliophora) in both intra- and inter-kingdom networks. Furthermore, the microbiome of diseased plants not only showed a higher relative abundance of functional genes related to bacterial anti-predator responses than healthy plants, but also contained a greater abundance of metagenome-assembled genomes with functional traits involved in this response. The increased microbial inter-kingdom associations between bacteria and protists, coupled with the notable bacterial anti-predator feedback in the microbiome of diseased plants, suggest that FWD may catalyse the associations between protists and their microbial prey. These findings highlight the potential role of predatory protists in influencing microbial assembly and functionality through top-down forces under pathogenic stress.

Effects of Different Manures in Combination with Fulvic Acid on the Abundance of N-Cycling Functional Genes in Greenhouse Soils

To investigate the effects of different manures in combination with fulvic acid on the abundance of N-cycling functional genes in greenhouse soils, Chinese cabbage was planted for three growing seasons. A total of six treatments—pig manure (P), pig manure + fulvic acid (PH), chicken manure (C), chicken manure + fulvic acid (CH), sheep manure (S), sheep manure + fulvic acid (SH) and no fertilization (CK)—were set up. The abundance of 13 soil N-cycling functional genes (gdhA, amoA-1, amoA-2, amoB, narG, nirK-1, nirK-2, nirK-3, nirS-1, nirS-2, nirS-3, nosZ and nifH) were investigated after the harvest of the third growing season using a gene chip approach. The results showed that fertilization treatments increased the abundance of most N-cycling functional genes in the soil, such as nitrification genes amoA-2 and amoB as well as denitrification genes narG, nirK-1, nirS-1 and nirS-2, with the stronger influence of sheep and pig manure than chicken manure. Fortunately, the additional fulvic acid reduced the increasing effect resulting from pig, chicken and sheep manure application. The abundance of functional genes for nitrogen cycling in soil was positively correlated with the content of soil organic matter, available phosphorus and NO3−-N, and negatively correlated with electrical conductivity. Overall, fertilization treatments increased soil nitrification and denitrification genes abundance, with a risk of increasing soil nitrogen loss, but the supplementary fulvic acid could limit the increase. In this study, it was concluded that the sheep manure (31.3 t/ha) + fulvic acid (7.5 kg/ha) treatment was more powerful in regulating the abundance of N-cycling functional genes in soil.

Marine toxin domoic acid alters nitrogen cycling in sediments

As a red tide algal toxin with intense neurotoxicity distributed worldwide, domoic acid (DA) has attracted increasing concerns. In this work, the integrative analysis of metagenome and metabolome are applied to investigate the impact of DA on nitrogen cycling in coastal sediments. Here we show that DA can act as a stressor to induce the variation of nitrogen (N) cycling by altering the abundance of functional genes and electron supply. Moreover, microecology theory revealed that DA can increase the role of deterministic assembly in microbial dynamic succession, resulting in the shift of niches and, ultimately, the alteration in N cycling. Notably, denitrification and Anammox, the important process for sediment N removal, are markedly limited by DA. Also, variation of N cycling implies the modification in cycles of other associated elements. Overall, DA is capable of ecosystem-level effects, which require further evaluation of its potential cascading effects.

Rhamnolipid-assisted solid-phase denitrification process for enhanced nitrate removal of recirculating mariculture system water

Solid-phase denitrification (SPD) is a promising approach for treating recirculating mariculture systems (RMS) water, but its relatively slow nitrate removal rate presents a challenge. This study, for the first time, investigates the enhanced nitrate removal in the SPD process by rhamnolipid (RL) addition. The enhancement by RL addition (20 and 40 mg L−1) was significant and largely persisted even after RL dosing was stopped. Specifically, the nitrate removal in RL-assisted SPD reactors was enhanced by 1.7–2.6 and 1.9–2.1 times for influent NO3−-N concentrations of 100 and 200 mg L−1, respectively. The enhancement was attributed to the improved biofilm formation, as indicated by the increased contents of biomass and extracellular polymeric substances. Moreover, the abundances of denitrification and biofilm formation functional bacteria (Pseudomonas and Denitromonas) also increased. RL addition increased abundances of functional genes involved in carbon degradation and nitrate removal. The denitrification and assimilatory nitrate reduction pathways achieved nitrate removal together. Therefore, RL-assisted SPD presents a novel strategy for treating nitrate-rich RMS water.

How do aeration mode and influent carbon/nitrogen ratio affect pollutant removal, gas emission, functional genes and bacterial community in subsurface wastewater infiltration systems?

Abstract This study investigated the influences of aeration mode and influent carbon/nitrogen ratio on matrix oxygen concentration, pollutant removal, greenhouse gas emission, functional gene abundances and bacterial community in subsurface wastewater infiltration systems (SWISs). Intermittent or continuous aeration enhanced oxygen supply at 0.6 m depth in the matrix, which improved organics removal, nitrogen removal, the abundances of bacterial 16S rRNA, amoA, nxrA, narG, napA, nirK, nirS, norB, nosZ genes, bacterial community Alpha diversity, the relative abundances of Actinobacteria at 0.6 m depth, the relative abundances of Chloroflexi, Gemmatimonadetes, Bacteroidetes and Firmicutes at 0.9 and 1.2 m depth and reduced CH4 and N2O conversion efficiencies, the abundance of mcrA gene with carbon/nitrogen ratio of 12 and 16 compared with non-aeration. Increased carbon/nitrogen ratio resulted in higher TN removal efficiencies and lower CH4 and N2O conversion efficiencies in aeration SWISs than those in non-aeration SWIS. Intermittent aeration SWIS obtained high removal efficiencies of 83.2, 85.4 and 90.8% for TN, NH4+ -N and COD and low conversion efficiency of 0.21 and 0.65% for N2O and CH4 with optimal carbon/nitrogen ratio of 12. However, high TN (82.6%), NH4+ -N (84.9%) and COD (92.2%) removal efficiencies and low CH4 (0.67%) and N2O (0.23%) conversion efficiencies were achieved in continuous aeration SWIS with carbon/nitrogen ratio of 16.

Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost

Microorganisms drive many aspects of organic carbon cycling in thawing permafrost soils, but the compositional trajectory of the post-thaw microbiome and its metabolic activity remain uncertain, which limits our ability to predict permafrost–climate feedbacks in a warming world. Using quantitative metabarcoding and metagenomic sequencing, we determined relative and absolute changes in microbiome composition and functional gene abundance during thaw incubations of wet sedge tundra collected from northern Alaska, USA. Organic soils from the tundra active-layer (0–50 cm), transition-zone (50–70 cm), and permafrost (70+ cm) depths were incubated under reducing conditions at 4 °C for 30 days to mimic an extended thaw duration. Following extended thaw, we found that iron (Fe)-cycling Gammaproteobacteria, specifically the heterotrophic Fe(III)-reducing Rhodoferax sp. and chemoautotrophic Fe(II)-oxidizing Gallionella sp., increased by 3–5 orders of magnitude in absolute abundance within the transition-zone and permafrost microbiomes, accounting for 65% of community abundance. We also found that the abundance of genes for Fe(III) reduction (e.g., MtrE) and Fe(II) oxidation (e.g., Cyc1) increased concurrently with genes for benzoate degradation and pyruvate metabolism, in which pyruvate is used to generate acetate that can be oxidized, along with benzoate, to CO2 when coupled with Fe(III) reduction. Gene abundance for CH4 metabolism decreased following extended thaw, suggesting dissimilatory Fe(III) reduction suppresses acetoclastic methanogenesis under reducing conditions. Our genomic evidence indicates that microbial carbon degradation is dominated by iron redox metabolism via an increase in gene abundance associated with Fe(III) reduction and Fe(II) oxidation during initial permafrost thaw, likely increasing microbial respiration while suppressing methanogenesis in wet sedge tundra.

Carbon nanosol-induced assemblage of a plant-beneficial microbiome consortium

Carbon nanosol (CNS) is a carbon-based nanomaterial that promotes plant growth; however, its functional mechanisms and effects on the microbiome are not fully understood. Here, we explored the effects of CNS on the relationship between the soil, endophytic microbiomes and plant productivity. CNS treatment increased the fresh biomass of tobacco (Nicotiana tabacum L.) plants by 27.4% ± 9.9%. Amplicon sequencing analysis showed that the CNS treatment significantly affected the composition and diversity of the microbial communities in multiple ecological niches associated with tobacco, especially the bulk soil and stem endophytic microbiome. Furthermore, the application of CNS resulted in enhanced network connectivity and stability of the microbial communities in different niches, particularly in the soil, implying a strengthening of certain microbial interactions. Certain potentially growth-promoting root endophytic bacteria were more abundant under the CNS treatment. In addition, CNS increased the abundance of some endophytic microbial functional genes known to enhance plant growth, such as those associated with nutrient metabolism and the plant hormone biosynthesis pathways. We isolated two bacterial strains (Sphingopyxis sp. and Novosphingobium sp.) that were enriched under CNS treatment, and they were confirmed to promote tobacco plant growth in vitro. These results suggested that CNS might, at least in part, promote plant growth by enriching beneficial bacteria in the microbiome.Graphical

Oligoagars and microbial agents show potential for Porphyra disease prevention

Disease is a major concern in Porphyra aquaculture, particularly during the early shell-borne conchocelis (SBC) seedling stage. To explore prevention strategies for Porphyra diseases, this study explored the potential of using oligoagars (OA) and microbial agents (MA) to treat SBC of Neoporphyra haitanensis in an aquaculture environment. The impact of these treatments on the phycosphere microbial community was analyzed, and the resistance of the treated Porphyra conchocelis to the pathogenic bacterium Vibrio mediterranei 117-T6 (which causes yellow spot disease) was tested in the lab. Results showed that OA reduced α-diversity while enriching Rhodobacteriaceae, and MA increased stability and relative abundance of Bacteroidetes (including Flavobacteria). Furthermore, compared to the control group, the abundance of pathogenic microorganisms and virulence functional genes decreased while defense-related functional gene abundance increased significantly in the groups treated with OA and MA. Most importantly, the OA and MA treatments improved resistance to Vm117-T6, with survival rates of 70% (OA) and 80% (MA), compared to 15% in the control group. Overall, the findings suggest that OA and MA treatments have great potential for preventing Porphyra disease, as they improve phycosphere microorganisms and increase algae resistance to pathogenic bacteria.

Distinct variabilities of soil abundant and rare bacteria relate differently to carbon cycling functionality in eroded ecosystems

Elucidating the interaction between microorganisms and soil carbon cycling functionality (SCCF) in the eroded ecosystems, can improve our understanding of the mechanisms by which soil erosion and deposition affect soil organic carbon pool. Abundant and rare sub-communities are the integral components in driving SCCF. However, changes in abundant and rare sub-communities, as well as their contributions to SCCF, remain unclear in the eroded ecosystems. In this study, changes in abundant and rare sub-communities and their correlations with SCCF were comparatively explored with respect to soil erosion and deposition in the Loess Plateau. The α-diversity of rare sub-communities in the depositional zones was 4% higher than that in the eroding slopes, but there was no significant difference in α-diversity of abundant sub-communities between the eroding slopes and depositional zones. The compositions of abundant and rare sub-communities differed between the eroding slopes and depositional zones. Regarding the co-occurrence network of the eroded ecosystems, abundant sub-communities compared with rare sub-communities presented a higher degree and betweenness centrality; however, rare sub-communities possessed more frequent interactions with other species than abundant sub-communities, especially positive interactions. The α-diversity of abundant and rare sub-communities in ecological clusters showed positive links with SCCF. The link between α-diversity of abundant sub-communities and SCCF was weaker than that with rare sub-communities, which was related to the significant disparity in the abundance of functional genes involved in SCCF and the extent of functional redundancy between abundant and rare sub-communities in the eroded ecosystems. The functional difference of abundant and rare sub-communities in improving SCCF under soil erosion and deposition, is important for accurately assessing the effects of microbial communities on soil organic carbon pool in regions predominated with fragmented eroded landscapes.

Riboflavin-loaded carbon cloth aids the anaerobic digestion of cow dung by promoting direct interspecies electron transfer

Cow dung generates globally due to increased beef and milk consumption, but its treatment efficiency remains low. Previous studies have shown that riboflavin-loaded conductive materials can improve anaerobic digestion through enhance direct interspecies electron transfer (DIET). However, its effect on the practical anaerobic digestion of cow dung remained unclear. In this study, carbon cloth loaded with riboflavin (carbon cloth-riboflavin) was added into an anaerobic digester treating cow dung. The carbon cloth-riboflavin reactor showed a better performance than other two reactors. The metagenomic analysis revealed that Methanothrix on the surface of the carbon cloth predominantly utilized the CO2 reduction for methane production, further enhanced after riboflavin addition, while Methanothrix in bulk sludge were using the acetate decarboxylation pathway. Furthermore, the carbon cloth-riboflavin enriched various major methanogenic pathways and activated a large number of enzymes associated with DIET. Riboflavin's presence altered the microbial communities and the abundance of functional genes relate to DIET, ultimately leading to a better performance of anaerobic digestion for cow dung.

The composition and function of the gut microbiota of Francois' langurs (Trachypithecus francoisi) depend on the environment and diet.

The microbiota is essential for the extraction of energy and nutrition from plant-based diets and may have facilitated primate adaptation to new dietary niches in response to rapid environmental shifts. In this study, metagenomic sequencing technology was used to analyze the compositional structure and functional differences of the gut microbial community of Francois' langurs (Trachypithecus francoisi) under different environmental and dietary conditions. The results showed that in terms of the composition of the gut microbial community, there were significant differences among the gut microbiota of Francois' langurs (anthropogenic disturbed populations, wild populations, and captive populations) under different environmental and dietary conditions. The microbial communities with the highest abundance in Francois' langurs were Firmicutes and Bacteroidetes. Firmicutes was the most abundant phylum in anthropogenic disturbed Francois' langurs and the least abundant in captive Francois' langurs. The abundance of Bacteroidetes was highest in captive Francois' langurs. In the analysis and comparison of alpha diversity, the diversity of the gut microbiota of Francois' langurs affected by anthropogenic disturbance was the highest. The significant differences in gut microbiota between Francois' langurs in different environments and different diets were further supported by principal coordinate analysis (PCoA), with the disturbance group having a gut microbiota more similar to the wild group. Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation analysis indicated a high abundance of functional genes involved in carbohydrate metabolism, amino acid metabolism, replication and repair, cofactor and vitamin metabolism, and other amino acid metabolism pathways. Additionally, the functional genes involved in carbohydrate metabolism pathways were significantly enriched in the gut microbial community of Francois' langurs that were anthropogenic disturbed and captive. The gut microbiota of the Francois' langurs exhibited potential plasticity for dietary flexibility, and long-term food availability in captive populations leads to changes in gut microbiota composition and function. This study explored the composition and function of the gut microbiota of Francois' langurs and provided a scientific basis for understanding the physiological and health status of Francois' langurs, effectively protecting the population of wild Francois' langurs and reintroducing captive Francois' langurs into the wild.

Biological inhibition of denitrification (BDI): an early plant strategy for Fallopia × bohemica seedling development.

The successful plant Fallopia × bohemica presents interesting capacities for control of the soil nitrogen cycle at the adult stage, termed biological inhibition of denitrification (BDI). The BDI strategy allows the plant, via the production of secondary metabolites (procyanidins), to compete with the denitrifying microbial community and to divert nitrate from the soil for its benefit. In this study, we analysed whether seedlings of F. × bohemica can implement BDI at the seedling stage. We also determined whether soil nitrogen availability influences the implementation of BDI and seedling growth. We sowed achenes of F. × bohemica in soils representing a nitrogen gradient (six treatments) and harvested seedlings after 20 or 40 days of growth. The denitrification and related microbial communities (i.e. functional gene abundances of nirK and nirS), soil parameters (nitrate content and humidity) and plant performance (biomass, growth and root morphology) were determined. On soil without addition of nitrogen, BDI was observed after 20 days of growth, whereas a stimulation of denitrification was found after 40 days. The increase of soil N content had few effects on the activity and structure of the soil denitrifying community and on the plant biomasses or the relative growth rates. Correlations between plant and microbial parameters were observed after 20 days of growth, reflecting early and strong chemical interactions between plants and the denitrifying community, which decreased with plant growth after 40 days. This study shows that an early BDI enhances the efficiency of nitrogen acquisition in the first weeks of growth, allowing for a conservative root strategy after 40 days. This switch to a conservative strategy involved resource storage, an altered allocation to above- and below-ground parts and an investment in fine roots. It now seems clear that this storage strategy starts at a very young age with early establishment of BDI, giving this clonal plant exceptional capacities for storage and multiplication.

Key genes of electron transfer, the nitrogen cycle and tetracycline removal in bioelectrochemical systems

BackgroundSoil microbial fuel cells (MFCs) can remove antibiotics and antibiotic resistance genes (ARGs) simultaneously, but their removal mechanism is unclear. In this study, metagenomic analysis was employed to reveal the functional genes involved in degradation, electron transfer and the nitrogen cycle in the soil MFC.ResultsThe results showed that the soil MFC effectively removed tetracycline in the overlapping area of the cathode and anode, which was 64% higher than that of the control. The ARGs abundance increased by 14% after tetracycline was added (54% of the amplified ARGs belonged to efflux pump genes), while the abundance decreased by 17% in the soil MFC. Five potential degraders of tetracycline were identified, especially the species Phenylobacterium zucineum, which could secrete the 4-hydroxyacetophenone monooxygenase encoded by EC 1.14.13.84 to catalyse deacylation or decarboxylation. Bacillus, Geobacter, Anaerolinea, Gemmatirosa kalamazoonesis and Steroidobacter denitrificans since ubiquinone reductase (encoded by EC 1.6.5.3), succinate dehydrogenase (EC 1.3.5.1), Coenzyme Q-cytochrome c reductase (EC 1.10.2.2), cytochrome-c oxidase (EC 1.9.3.1) and electron transfer flavoprotein-ubiquinone oxidoreductase (EC 1.5.5.1) served as complexes I, II, III, IV and ubiquinone, respectively, to accelerate electron transfer. Additionally, nitrogen metabolism-related gene abundance increased by 16% to support the microbial efficacy in the soil MFC, and especially EC 1.7.5.1, and coding the mutual conversion between nitrite and nitrate was obviously improved.ConclusionsThe soil MFC promoted functional bacterial growth, increased functional gene abundance (including nitrogen cycling, electron transfer, and biodegradation), and facilitated antibiotic and ARG removal. Therefore, soil MFCs have expansive prospects in the remediation of antibiotic-contaminated soil. This study provides insight into the biodegradation mechanism at the gene level in soil bioelectrochemical remediation.

Discrepant responses of bacterial community and enzyme activities to conventional and biodegradable microplastics in paddy soil

The prevalence of microplastics in soil ecosystems has raised concerns about their potential effects on soil properties. As promising alternatives to conventional plastics, biodegradable plastics have been increasingly applied in agricultural activities, which may release microplastics into the soil due to incomplete degradation. Compared to conventional microplastics, biodegradable microplastics in soil may induce different impacts on soil microbial properties, which have yet to be well studied. Through a 41-day microcosm experiment, we evaluated the differential effects of conventional (polypropylene, PP) and biodegradable (polylactic acid, PLA) microplastics on the geochemical properties, enzyme activities, and microbial community structure in paddy soil. Adding PLA or PP microplastics into soil significantly increased pH values and altered the contents of carbon and nitrogen nutrients. Exposure to microplastics significantly increased the activity of fluorescein diacetate hydrolase, but had varying effects on the activities of urease, sucrase, and alkaline phosphatase depending on microplastic types and doses. The addition of microplastics also influenced the structure of soil bacterial community, with Proteobacteria, Actinobacteriota, and Acidobacteriota being the dominant phyla. Significant differences in the genera of Pseudarthrobacter, Acidothermus, Bacillus, Aquisphaera, and Massilia were observed between treatments. Results of structural equation modeling (SEM) demonstrated that changes in soil carbon and nitrogen nutrients and pH values positively affected the bacterial community, while soil bacterial community as a whole exerted a negative impact on enzyme activities. FAPRPTAX analysis showed that the addition of microplastics altered the relative abundances of functional genes related to the metabolism of cellulose decomposition and ureolysis in paddy soil. Findings of this study clearly suggest that microplastic impacts on soil geochemical and microbial properties should be an integral part of future risk assessment and that to evaluate microplastic impacts, both the concentration and polymer type must be taken into account.

Simultaneously enhanced autotrophic–heterotrophic denitrification in iron-based ecological floating bed by plant biomass: Metagenomics insights into microbial communities, functional genes and nitrogen metabolic pathways

In this study, the ecological floating bed supporting with zero-valent iron (ZVI) and plant biomass (EFB-IB) was constructed to improve nitrogen removal from low-polluted water. The effects of ZVI coupling with plant biomass on microbial community structure, metabolic pathways and functional genes were analyzed by metagenomic sequencing, and the mechanism for nitrogen removal was revealed. Results showed that compared with mono-ZVI system (EFB-C), the denitrification efficiencies of EFB-IB were effectively enhanced, with the higher average NO3−-N removal efficiencies of 22.60–59.19%. Simultaneously, the average NH4+-N removal efficiencies were 73.08–91.10%. Metagenomic analyses showed that EFB-IB enriched microbes that involved in iron cycle, lignocellulosic degradation and nitrogen metabolism. Plant biomass addition simultaneously increased the relative abundances of autotrophic and heterotrophic denitrifying bacteria. Network analysis showed the cooperation between autotrophic and heterotrophic denitrifying bacteria in EFB-IB. Moreover, compared with EFB-C, plant biomass addition increased the relative abundances of genes related to iron cycle, lignocellulose degradation and glycolysis processes, ensuring the production of autotrophic and heterotrophic electron donors. Therefore, the relative abundances of key enzymes and functional genes related to denitrification were higher in EFB-IB, being beneficial to the NO3−-N removal. Additionally, the correlation analysis of nitrogen removal and functional genes verified the synergistic mechanism of iron-based autotrophic denitrification and plant biomass-mediated heterotrophic denitrification in EFB-IB. In summary, plant biomass has excellent potential to improve the nitrogen removal of iron-based EFB from low-polluted water.

Divergent effects of biochar amendment and replacing mineral fertilizer with manure on soil respiration in a subtropical tea plantation

Applying biochar amendment and manure in tea plantation ecosystems can diminish soil acidification and degradation. However, the impact of these practices on soil respiration and associated mechanisms remains unclear. In this study, we combined a two-year field experiment and laboratory analyses based on soil properties, functional genes, and microbial co-occurrence networks to explore the determinants of soil respiration intensity in a subtropical tea plantation with biochar amendment and manure application. The results showed that the effect of biochar amendment on soil respiration was unconspicuous. Although biochar amendment increased bacterial richness and Shannon index, biochar amendment did not alter the abundance of species associated with C-cycling functional genes. Besides directly adding recalcitrant C to the soil, biochar also indirectly enhanced C sequestration by weakly increasing soil carbon dioxide (CO2) emissions. However, replacing mineral fertilizer with manure significantly stimulated soil respiration in the tea plantation, resulting in a 36% increase in CO2 emissions over two years. The increase in CO2 emissions under the manure treatment was mainly attributed to the increased soil labile C pool, the activity of hydrolytic enzymes (e.g., cellobiohydrolase and acetylglucosaminidase), and the relative abundance of functional genes associated with the C-cycle. This may also be related to the application of manure that increased the abundance of Gemmatimonadetes and altered ecological clusters in bacterial co-occurrence networks. Our correlation network analysis suggested that Gemmatimonadetes might be the potential hosts for C-cycling genes due to their strong positive correlation with the abundance of C-cycling genes. Overall, these findings provide new insights into soil respiration under biochar amendment and manure application in tea plantations and broaden the options for carbon sequestration in soils.Graphical

In-depth insight into improvement of simultaneous nitrification and denitrification/biofouling control by increasing sludge concentration in membrane reactor: performance, microbial assembly and metagenomic analysis

Currently, severe membrane fouling and inefficient nitrogen removal were two main issues that hindered the sustainable operation and further application of membrane bioreactor (MBR). This study aimed to simultaneously alleviate membrane fouling and improve nitrogen removal by applying high sludge concentration in MBR. Results showed that high sludge concentration (12000 mg/L) enhanced total nitrogen removal efficiency (78 %) and reduced transmembrane pressure development rate. Microbial community analysis revealed that high sludge concentration enriched functional bacteria associated with nitrogen removal, increased filamentous bacteria fraction in bio-cake and inhibited Thiothrix overgrowth in bulk sludge. From molecular level, the key genes involved in nitrogen metabolism, electron donor/adenosine triphosphate production and amino acid degradation were up-regulated under high sludge concentration. Overall, high sludge concentration improved microbial assembly and functional gene abundance, which not only enhanced nitrogen removal but also alleviated membrane fouling. This study provided an effective strategy for sustainable operation of MBR.

Impacts of substrate properties and aquatic nutrient concentrations on the relative abundance of nitrifying/denitrifying genes and the associated microbes in epilithic biofilms.

Substrates like sand or gravels and aquatic nutrient concentrations of rivers are highly heterogeneous, influencing the abundance of functional genes in epilithic biofilms where nitrification-denitrification processes take place. To analyze how the relative abundance of nitrifying/denitrifying genes and the associated microbes changes with the physical properties of substrates and aquatic concentrations of nutrients, this paper utilized metagenomics to comprehensively characterize these functional genes (i.e., amoA, hao, and nxrB involved in nitrification, and napA, narG, nirS, norB, and nosZ associated with denitrification) from epilithic biofilms collected along the Shitingjiang River in Southwest China and further obtained the relative abundance of major nitrifiers and denitrifiers. The results show that substrate size most significantly affects the relative abundance of hao and norB by altering the hydrodynamic conditions. In sampling sites with high heterogeneity in substrate size distribution, the relative abundance of most denitrifying genes is also higher. The carbon-nitrogen ratio negatively correlates with the relative abundance of all the nitrifying genes, while ammonium, total inorganic carbon, and total organic carbon concentrations positively affect the relative abundance of amoA and nxrB. As to the relative abundance of nitrifiers and denitrifiers, mainly belonging to phyla Proteobacteria and Actinobacteria, substrate heterogeneity and the aquatic concentrations of nutrients have greater influences than substrate size. Also, the substrate heterogeneity exerted positive influence on functional species of Pseudogemmobacter bohemicus and Paracoccus zhejiangensis. Considering the genes' functions and the dominant species linked to denitrification, nitrous oxide is more likely to occur in rivers with higher heterogeneity and larger substrates.