rDNA- and rRNA-derived communities present divergent assemblage patterns and functional traits throughout full-scale landfill leachate treatment process trains

Conversion of monocropping to intercropping promotes rhizosphere microbiome functionality and soil nitrogen cycling

Intercropping can increase soil nutrient availability and provide greater crop yields for intensive agroecosystems. Despite its multiple benefits, how intercropping influences rhizosphere microbiome assemblages, functionality, and complex soil nitrogen cycling is not fully understood. Here, a three-year field experiment was carried out on different cropping system with five fertilization treatments at the main soybean production regions. We found that soybean yields in intercropped systems were on average 17 % greater than in monocropping system, regardless of fertilization treatments. We also found that intercropping systems significant increased network modularity (by 46 %) and functional diversity (by 11 %) than monocropping systems. Metagenomics analyses further indicated intercropping promotes microbiome functional adaptation, particularly enriching core functions related to nitrogen metabolism. Cropping patterns had a stronger influence on the functional genes associated with soil nitrogen cycling (R2 = 0.499). Monocropping systems increased the abundance of functional genes related to organic nitrogen ammonification, nitrogen fixation, and denitrification, while functional guilds of nitrate assimilation (by 28 %), nitrification (by 31 %), and dissimilatory nitrate reduction (by 10.1 %) genes were enriched in intercropping systems. Furthermore, we found that abiotic factors (i.e. AP, pH, and Moisture) are important drivers in shaping soil microbial community assemblage and nitrogen cycling. The functional genes include hzsB, and nrfA, and nxrA that affected by these biotic and abiotic variables were strongly related to crop yield (R2 = 0.076 ~ R2 = 0.249), suggesting a key role for maintaining crop production. We demonstrated that land use conversion from maize monocropping to maize-soybean intercropping diversify rhizosphere microbiome and functionality signatures, and intercropping increased key gene abundance related to soil nitrogen cycling to maintain the advantage of crop yield. The results of this study significantly facilitate our understanding of the complex soil nitrogen cycling processes and lay the foundation for manipulating desired specific functional taxa for improved crop productivity under sustainable intensification.

Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species

Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O₂ (~7%). The cave's surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O₂ and NO₃^- as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.

Exploration of β-glucosidase-producing microorganisms community structure and key communities driving cellulose degradation during composting of pure corn straw by multi-interaction analysis

Poor management of crop residues leads to environmental pollution and composting is a sustainable practice for addressing the challenge. However, knowledge about composting with pure crop straw is still limited, which is a novel and feasible composting strategy. In this study, pure corn straw was in-situ composted for better management. Community structure of β-glucosidase-producing microorganisms during composting was deciphered using high-throughput sequencing. Results showed that the compost was mature with organic matter content of 37.83% and pH value of 7.36 and pure corn straw could be composted successfully. Cooling phase was major period for cellulose degradation with the highest β-glucosidase activity (476.25 μmol·p-Nitr/kg·dw·min) and microbial diversity (Shannon index, 3.63; Chao1 index, 500.81). Significant compositional succession was observed in the functional communities during composting with Streptomyces (14.32%), Trichoderma (13.85%) and Agromyces (11.68%) as dominant genera. β-Glucosidase-producing bacteria and fungi worked synergistically as a network to degrade cellulose with Streptomyces (0.3045**) as the key community revealed by multi-interaction analysis. Organic matter (-0.415***) and temperature (-0.327***) were key environmental parameters regulating cellulose degradation via influencing β-glucosidase-producing communities, and β-glucosidase played a key role in mediating this process. The above results indicated that responses of β-glucosidase-producing microorganisms to cellulose degradation were reflected at both network and individual levels and multi-interaction analysis could better explain the relationship between variables concerning composting cellulose degradation. The work is of significance for understanding cellulose degradation microbial communities and process during composting of pure corn straw.

Disentangling the coupling relationships between functional denitrifiers and nitrogen transformation during cattle-manure and biochar composting: A novel perspective

This study explored the coupling relationships between denitrifiers and N-transformation using multi-level (DNA, RNA and enzyme) and multi-aspect (abundance, diversity, structure, key community, network pattern, and functional module) analyses during cattle-manure (CM) and biochar (CMB) composting. Amino sugar-N (ASN, 0.914) and hydrolysable unknown-N (-0.724) were main organic-N components mediating NH₄⁺-N in CM and CMB, respectively. Biochar lowered nirK, nirS, and nosZ genes copies, up-regulated nir gene transcripts, and inhibited nitrite reductase (NIR) activity. For nirK-denitrifiers, Luteimonas was predominant taxa influencing NO₂^--N and amino acid-N (AAN). Unclassified_k_norank_d_Bacteria and unclassified_p_Proteobacteria regulated NO₃^--N and ASN, respectively. These three genera played crucial roles in mediating NIR activity and nosZ/nirK. For nirS-denitrifiers, Paracoccus and Pseudomonas mediated NH₄⁺-N and AAN, respectively, and they were vital genera regulating NO₃^--N, ASN and NIR activity. Furthermore, nirK-denitrifiers was major contributor to denitrification. Overall, functional denitrifiers might simultaneously participate in multiple N-transformation processes.

Continuous plug-flow anammox system for mature landfill leachate treatment: Key zone for anammox pathway

This study established the one-stage partial nitrification coupled anammox and partial denitrification coupled anammox process in an anoxic/oxic continuous plug-flow system and operated for 465 days to treat mature landfill leachate. 97.9 %-98.1 % of inorganic nitrogen was removed when the nitrogen loading rate was maintained at 0.33-0.36 kg N/m³/d, and a high anammox contribution to nitrogen removal (89.8 %-92.4 %) was achieved. The long-term in-situ free ammonia (FA) anoxic treatment contributed to the stable performances of partial nitrification and in-situ fermentation. The employed integrated fixed-film activated sludge technology favored the enrichment of hzsA, hzsB, hdh, amoA, hao, narG, and napA functional genes. The oxic zone, particularly oxic biofilm, was the key zone for anammox pathway, where Candidatus_Kuenenia (from 1.6 % to 8.3 %) with high tolerance to FA and salinity stress outcompeted Candidatus_Brocadia (from 18.3 % to 0.1 %) as the dominant anammox bacteria. This study could provide guidance for anammox-mediated landfill leachate treatment in practical projects.

Exploratory analysis of the microbial community profile of the municipal solid waste leachate treatment system: A case study

Studies on the degradation dynamics of landfill leachate indicate that the microbial community profile is a valuable and sensitive tool for landfill monitoring programs. Although knowledge about the microbial community can improve the efficiency of leachate treatment systems, little is known about the microbial profile changes that occur throughout the leachate attenuation process. In the present work, an exploratory analysis of the microbial community profile of the MSW leachate treatment system in the municipality of Osório (Brazil) was conducted. In this way, a comprehensive analysis of chemical parameters, isotopic signature and microbial profile data were applied to monitor the changes in the structure of the microbial community throughout the leachate attenuation process and to describe the relationship between the microbial community structure and the attenuation of chemical and isotopic parameters. From data analysis, it was possible to assess the microbial community structure and relate it to the attenuation of chemical and isotopic parameters. Based on massive parallel 16S rRNA gene sequencing, it was possible to observe that each leachate treatment unit has a specific microbial consortium, reflecting the adaptation of different microorganisms to changes in leachate characteristics throughout treatment. From our results, we concluded that the structure of the microbial community is sensitive to the leachate composition and can be applied to study the municipal solid waste management system.

Inter-phylum negative interactions affect soil bacterial community dynamics and functions during soybean development under long-term nitrogen fertilization

Understanding interspecies interactions is essential to predict the response of microbial communities to exogenous perturbation. Herein, rhizospheric and bulk soils were collected from five developmental stages of soybean, which grew in soils receiving 16-year nitrogen inputs. Bacterial communities and functional profiles were examined using high-throughput sequencing and quantitative PCR, respectively. The objective of this study was to identify the key bacterial interactions that influenced community dynamics and functions. We found that the stages of soybean development outcompeted nitrogen fertilization management in shaping bacterial community structure, while fertilization treatments significantly shaped the abundance distribution of nitrogen functional genes. Temporal variations in bacterial abundances increased in bulk soils, especially at the stage of soybean branching, which helps to infer underlying negative interspecies interactions. Members of Cyanobacteria and Actinobacteria actively engaged in inter-phylum negative interactions in bulk soils and soybean rhizosphere, respectively. Furthermore, the negative interactions between nitrogen-fixing functional groups and the reduction of nifH gene abundance were coupled during soybean development, which may help to explain the linkages between population dynamics and functions. Overall, these findings highlight the importance of inter-phylum negative interactions in shaping the correlation patterns of bacterial communities and in determining soil functional potential.

Understanding Microbial Arsenic-Mobilization in Multiple Aquifers: Insight from DNA and RNA Analyses

Biogeochemical processes critically control the groundwater arsenic (As) enrichment; however, the key active As-mobilizing biogeochemical processes and associated microbes in high dissolved As and sulfate aquifers are poorly understood. To address this issue, the groundwater-sediment geochemistry, total and active microbial communities, and their potential functions in the groundwater-sediment microbiota from the western Hetao basin were determined using 16S rRNA gene (rDNA) and associated 16S rRNA (rRNA) sequencing. The relative abundances of either sediment or groundwater total and active microbial communities were positively correlated. Interestingly, groundwater active microbial communities were mainly associated with ammonium and sulfide, while sediment active communities were highly related to water-extractable nitrate. Both sediment-sourced and groundwater-sourced active microorganisms (rRNA/rDNA ratios > 1) noted Fe(III)-reducers (induced by ammonium oxidation) and As(V)-reducers, emphasizing the As mobilization via Fe(III) and/or As(V) reduction. Moreover, active cryptic sulfur cycling between groundwater and sediments was implicated in affecting As mobilization. Sediment-sourced active microorganisms were potentially involved in anaerobic pyrite oxidation (driven by denitrification), while groundwater-sourced organisms were associated with sulfur disproportionation and sulfate reduction. This study provides an extended whole-picture concept model of active As-N-S-Fe biogeochemical processes affecting As mobilization in high dissolved As and sulfate aquifers.

Insight into the influence of biochar on nitrification based on multi-level and multi-aspect analyses of ammonia-oxidizing microorganisms during cattle manure composting

In this study, influence of biochar on nitrification was explored using multi-level (DNA, RNA, protein) and multi-aspect (diversity, structure, key community, co-occurrence pattern and functional modules) analyses (M-LAA) of ammonia-oxidizing microorganisms (AOMs) during cattle manure composting. Biochar addition increased the copy numbers and diversity of AOMs, restricted (36.02%) the amoA gene transcripts of archaea but increased (24.53%) those of bacteria, and reduced (75.86%) ammonooxygenase (AMO) activity. Crenarchaeota and Thaumarcheota mediated NH4+-N, Unclassified_k_norank_d_Archaea and Crenarchaeota regulated AMO activity and potential ammonia oxidation (PAO) rates. Nitrosomonas and Nitrosospira were the predominant microbial taxa influencing NH4+-N variation and PAO rates, respectively. Additionally, both Crenarchaeota and Nitrosospira played crucial roles in mediating NO3--N and NO2--N. Furthermore, biochar altered the network patterns of AOMs community by changing the keystone species and the interactivity among communities. These findings indicated that influence of biochar on nitrification could be better explained using M-LAA of AOMs.

Metagenomic Insights Into Functional and Taxonomic Compositions of an Activated Sludge Microbial Community Treating Leachate of a Completed Landfill: A Pathway-Based Analysis

Upcycling wastes into valuable products by mixed microbial communities has recently received considerable attention. Sustainable production of high-value substances from one-carbon (C1) compounds, e.g., methanol supplemented as an external electron donor in bioreactors for wastewater treatment, is a promising application of upcycling. This study undertook a gene-centric approach to screen valuable production potentials from mixed culture biomass, removing organic carbon and nitrogen from landfill leachate. To this end, the microbial community of the activated sludge from a landfill leachate treatment plant and its metabolic potential for the production of seven valuable products were investigated. The DNA extracted from the activated sludge was subjected to shotgun metagenome sequencing to analyze the microbial taxonomy and functions associated with producing the seven products. The functional analysis confirmed that the activated sludge could produce six of the valuable products, ectoine, polyhydroxybutyrate (PHB), zeaxanthin, astaxanthin, acetoin, and 2,3-butanediol. Quantification of the detected functional gene hit numbers for these valuable products as a primary trial identified a potential rate-limiting metabolic pathway, e.g., conversion of L-2,4-diaminobutyrate into N-γ-acetyl-L2,4,-diaminobutyrate during the ectoine biosynthesis. Overall, this study demonstrated that primary screening by the proposed gene-centric approach can be used to evaluate the potential for the production of valuable products using mixed culture or single microbe in engineered systems. The proposed approach can be expanded to sites where water purification is highly required, but resource recovery, or upcycling has not been implemented.

Simple assay for colorimetric quantification of unamplified bacterial 16S rRNA in activated sludge using gold nanoprobes

Domestic and industrial wastewater treatment systems are vital in the protection of natural ecosystems and human health. Identification of microbial communities in the systems is essential to stable treatment performance. However, the current tools of microbial community analysis are labor intensive and time consuming, and require expensive equipment. Therefore, we developed a simple assay for colorimetric quantification of bacterial 16S rRNA extracted from environmental samples. The assay is based on RNA extraction with commercial kits, mixing the unamplified RNA sample with Au-nanoprobes and NaCl, and analyzing the absorbance spectra. Our experimental results confirmed that the assay format was valid. By analyzing the synthesized DNA, we optimized the operational parameters affecting the assay. We achieved adequate capture DNA density by setting the capture DNA probe concentration at 10 μM during the functionalization step. The required incubation time after NaCl addition was 30 min. The binding site of the target had negligible effect on DNA detection. Under the optimized condition, a calibration curve was created using 16S rRNA extracted from activated sludge. The curve was linear above 5.0 × 10⁷ copies/μL of bacterial 16S rRNA concentration, and the limit of detection was 1.17 × 10⁸ copies/μL. Using the calibration curve, the bacterial 16S rRNA concentration in activated sludge samples could be quantified with deviations between 48% and 208% against those determined by RT-qPCR. The findings of our study introduce an innovative tool for the quantification of 16S rRNA concentration as the activity of key bacteria in wastewater treatment processes, achieving stable treatment performance.

Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes

We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by Bacteroidetes and Firmicutes. We identified 2210 common genes in the two groups. LEfSe showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.

Autoinducer-2-mediated quorum sensing partially regulates the toxic shock response of anaerobic digestion

This study discovered a strong correlation between the autoinducer-2 (AI-2)-mediated quorum sensing (QS) with the performance of a submerged anaerobic membrane bioreactor during its recovery from a pentachlorophenol (PCP) shock: a decrease in AI-2 levels coincided with a reduction in volatile fatty acid concentrations, and corresponded significantly to a decrease in the relative abundance of Firmicutes, and to an increase in the relative abundance of Bacteroidetes and Synergistetes. Further batch experiments with the addition of an AI-2-regulating Escherichia coli mutant culture showed that a reduction in AI-2 levels resulted in the highest biogas production rate during a PCP shock. In contrast, an increase in AI-2 levels via addition of the E. coli wild type strain or an AI-2 precursor showed no obvious effects on biogas production. These results suggest that the AI-2 level in anaerobic sludge was governed primarily by Firmicutes, and the AI-2-mediated QS partially regulates the toxic shock response of anaerobic sludge via tuning the activities of Firmicutes and Synergistetes. A decrease in the AI-2 level might reduce acetogenesis and favor hydrogenotrophic methanogenesis, thus resulting in less VFA accumulation and higher methane production during the PCP shock. This study is the first of this type that exploits the role of quorum sensing in the toxic shock response of anaerobic sludge; it demonstrates a novel approach to shortening the recovery period of anaerobic processes via manipulating the AI-2-mediated QS.

Process stability and comparative rDNA/rRNA community analyses in an anaerobic membrane bioreactor with silicon carbide ceramic membrane applications

This study evaluated the feasibility of using a silicon carbide (SiC) anaerobic ceramic membrane bioreactor (AnCMBR) to co-manage domestic wastewater (DWW) and food waste recycling wastewater (FRW). A pilot-scale SiC-AnCMBR was put into operation for 140 days under two different organic loading rates (OLRs): 5 kg COD m^-3 d^-1 (OLR 5) and 3 kg COD m^-3 d^-1 (OLR 3). The organic removal efficiency was 93.5 ± 3.7% over the operational period. Methane production increased significantly after sludge re-seeding at OLR 3. rDNA and rRNA microbial results showed that the active archaeal community was affected by sludge re-seeding, whereas the active bacterial community was not, indicating that a shift in the active archaeal community was responsible for the increased methane production. Our results thus suggest that SiC-AnCMBRs are a promising option for co-managing DWW and FRW.