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Swine manure is considered to be a reservoir for antibiotic resistance genes (ARGs) but little is known about the variations in ARGs during the co-composting of swine manure with Chinese medicinal herbal residues (CMHRs). Thus, this study explored the effects of CMHRs on the variations in ARGs during co-composting with swine manure. The results showed that CMHRs could reduce effectively most of the targeted ARGs (0.18–2.82 logs) and mobile genetic elements (MGEs) (0.47–3.34 logs). The correlations indicated that CMHRs might decrease the spread of ARGs via horizontal gene transfer. Redundancy analysis showed that the bacterial communities had more important effects on the variations in ARGs compared with environmental factors and MGEs. The results of this study demonstrate that CMHRs can decrease the abundances of ARGs and MGEs, as well as reducing the risk of ARGs spreading during the application of compost products to farmland. [ABSTRACT FROM AUTHOR]

Superabsorbent polymers (SAPs) are considered suitable amendments for reducing the selection pressure due to heavy metals and the abundances of antibiotic resistance genes (ARGs) during composting. In this study, three SAP (sodium polyacrylate) levels (0, 5, and 15 mg kg −1 of compost) were applied and their effects on the abundances of ARGs, mobile genetic elements (MGEs), and the bacterial community were investigated. After composting, the abundances of ARGs and MGEs decreased to different extent, where the removal efficiencies for tetW , dfrA7 , ermX , aac(6′)-ib-cr and MGEs exceeded 90%. The high SAP concentration significantly reduced the abundances of ARGs and MGEs, and changed the microbial community. Redundancy analysis indicated that the moisture content mainly explained the changes in ARGs and MGEs. Network analysis determined the potential hosts of ARGs and MGEs, and their co-occurrence. The results suggested that applying 15 mg kg −1 SAP is appropriate for reducing ARGs in compost. [ABSTRACT FROM AUTHOR]

[Display omitted] • Inoculation enhanced the nifH gene and nitrogenase abundance in composting product. • Microbial inoculation yielded a richer and more diverse diazotroph community. • Inoculation changed the composition of the keystone species in composting system. • nifH gene abundance affected by carbon sources and diazotroph community succession. Diazotroph community contributes to the nitrogen mass and improves the agronomic quality of composting product, but their responses to microbial inoculation during composting are unclear. In this study, the lignocellulose-degrading consortium was inoculated at different levels (0%: CK (control) and 10%: T) to investigate their effects on the variations in the diazotroph community and functional gene during composting. In the later composting phase, the nifH gene copy number was 17.50−25.28% higher in T than CK. The nitrogenase abundance in CK and T were 0.042% and 0.046% in composting product, respectively. Network analysis indicated that inoculation affected the co-occurrence patterns of the diazotroph community and changed the keystone species composition. Partial least-squares path modeling showed that available carbon sources and the succession of the diazotroph community mainly determined the increased abundance of nifH gene. Microbial inoculation stimulated the diazotrophs activities, and was conducive to the nitrogen production in composting product. [ABSTRACT FROM AUTHOR]

• MAR improved the efficiency of reducing the relative abundances of ARGs and MGEs. • MGEs were mainly responsible for the changes in the abundances of ARGs. • ARGs and MGEs have the same potential host bacteria. • MAR added at 5% can reduce the risk of ARGs in swine manure composting. Swine manure is considered a reservoir for antibiotic resistance genes (ARGs), which may enter the soil and then the food chain to endanger human health. This study investigated the effects of adding 0%, 5%, and 15% (w/w) macroporous adsorption resin (MAR) on ARGs and the bacterial community during composting. The results showed that the addition of MAR reduced the abundances of ARGs (14.14–99.44%) and mobile genetic elements (MGEs) (47.83–99.48%) after swine manure composting. Significant positive correlations were detected between ARGs and MGEs, and thus the variations in MGEs may have led to the changes in ARGs. Redundancy analysis showed that MGEs had stronger effects on ARGs than environmental factors and the bacterial community. Network analysis suggested that ARGs and MGEs co-existed in common host bacteria. In conclusion, the results showed that adding 5% MAR can reduce the risk of ARG transmission. [ABSTRACT FROM AUTHOR]

• Microbial inoculation enhanced the diversity and richness of the fungal community. • Inoculation changed the co-occurrence patterns of the fungal community. • Inoculation led to higher abundances of the 18S rRNA and cellulose-degrading genes. • Variations in cellulose-degrading genes were driven by fungal community succession. Composting is used widely for recycling spent mushroom substrate (SMS). This study investigated the effects of inoculating a lignocellulose-degrading consortium at two levels comprising 0% (control: CK) and 10% (T) on the fungal community and cellulose-degrading genes during SMS co-composting with swine manure. Lignocellulose degradation rate in T was 8.77–34.45% higher compared with CK. Inoculation affected the distribution of the fungal community, increased the community diversity, and inhibited pathogens. Network analysis showed that inoculation changed the co-occurrence patterns of the fungal communities and made the co-composting system more stable. The relative abundances of glycoside hydrolase genes GH3E (fungal GH3), GH6 , and GH7 were 0.45, 0.09, and 0.39 logs higher in T, respectively, than CK. Partial least-squares path modeling suggested that the variations in cellulose-degrading genes were driven mainly by changes in the fungal community during co-composting. Therefore, the lignocellulose-degrading consortium accelerated the transformation of lignocellulose to facilitate safer composting. [ABSTRACT FROM AUTHOR]

Applying exogenous additives during the aerobic composting of livestock manure is effective for slowing down the spread of antibiotic resistance genes (ARGs) in the environment. Nanomaterials have received much attention because only low amounts need to be added and they have a high capacity for adsorbing pollutants. Intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs) comprise the resistome in livestock manure but the effects of nanomaterials on the fates of these different fractions during composting are still unclear. Thus, we investigated the effects of adding SiO 2 nanoparticles (SiO 2 NPs) at four levels (0 (CK), 0.5 (L), 1 (M), and 2 g/kg (H)) on i-ARGs, e-ARGs, and the bacterial community during composting. The results showed that i-ARGs represented the main fraction of ARGs during aerobic composting of swine manure, and their abundance was lowest under M. Compared with CK, M increased the removal rates of i-ARGs and e-ARGs by 17.9% and 100%, respectively. SiO 2 NPs enhanced the competition between ARGs hosts and non-hosts. M optimized the bacterial community by reducing the abundances of co-hosts (Clostridium_sensu_stricto_1 , Terrisporobacter , and Turicibacter) of i-ARGs and e-ARGs (by 96.0% and 99.3%, respectively) and killing 49.9% of antibiotic-resistant bacteria. Horizontal gene transfer dominated by mobile genetic elements (MGEs) played a key role in the changes in the abundances of ARGs. i- intI1 and e-Tn 916/1545 were key MGEs related closely to ARGs, and the maximum decreases of 52.8% and 100%, respectively, occurred under M, which mainly explained the decreased abundances of i-ARGs and e-ARGs. Our findings provide new insights into the distribution and main drivers of i-ARGs and e-ARGs, as well as demonstrating the possibility of adding 1 g/kg SiO 2 NPs to reduce the propagation of ARGs. [Display omitted] • Fates of antibiotic resistance genes (ARGs) with SiO 2 nanoparticles (SiO 2 NPs). • Intracellular ARGs (i-ARGs) more abundant than extracellular ARGs (e-ARGs). • Adding 1 g/kg SiO 2 NPs effective at reducing abundances of i-ARGs and e-ARGs. • SiO 2 NPs reduced risk of ARGs transmission by removing potential host bacteria. • i- intI1 and e-Tn 916/1545 crucial for reducing abundances of i-ARGs and e-ARGs. [ABSTRACT FROM AUTHOR]

Highlights • Coal gasification slag can enhance the removal of ARGs and MGEs from swine manure. • Decreases in ARGs may be due to reductions in abundances of potential host bacteria. • Bacterial succession responsible for variations in the ARG profiles. • Coal gasification slag added at 10 g/L can reduce the risk of ARGs in swine manure. Abstract Coal gasification slag (GS) is an industrial solid waste with a highly developed pore structure, which can be used in anaerobic digestion (AD) to remove antibiotic resistance genes (ARGs) due to its structure, thereby utilizing this waste resource. This study evaluated the effects of three GS levels (0, 5, and 10 g/L) on the abundances of ARGs, mobile genetic elements, and the bacterial community. With GS added at 10 g/L, the removal rates for ARGs (dfrA7 , sul2 , tetW , ermF , and ermQ) were 24.81–90.48% after AD, and the removal rate for ISCR1 was 95.4%. In addition, 10 g/L GS was more effective at reducing the abundances of potential human pathogens. The variations in ARGs may have been affected by the succession of the microbial community. The results of this study demonstrate that supplementation with 10 g/L GS is more useful for reducing ARGs during AD. [ABSTRACT FROM AUTHOR]

Highlights • Coal gasification slag (CGS) is one of the waste products. • CGS effectively reduced most ARGs and MGEs in swine manure compost. • Fourteen genera were identified as possible hosts of various ARGs. • Adding 10% CGS is a cost-effective option for reducing the abundance of ARGs. Abstract This study investigated the effects of the addition of coal gasification slag (CGS) at three levels (0%, 5%, and 10% w/w) on antibiotic resistance genes (ARGs) and the bacterial community during composting. The addition of CGS effectively facilitated the removal of ARGs and mobile genetic elements (MGEs), where it significantly reduced the relative abundances of 5/11 ARGs and three MGEs in the swine manure composting product. In addition, the enrichment of ARGs and intI1 was lower under the addition of 10% CGS compared with 0% CGS. The bacterial community was distributed according to the composting time under different treatments. Redundancy analysis showed that bacterial community succession and MGE-mediated horizontal gene transfer played important roles in the variations in ARGs. Network analysis indicated the co-occurrence of ARGs and MGEs with specific microorganisms. Thus, 10% CGS may be a suitable additive for reducing the risks of ARGs in compost products. [ABSTRACT FROM AUTHOR]

Understanding the main drivers that affect the spread of antibiotic resistance genes (ARGs) during the composting process is important for the removal of ARGs. In this study, three levels of tylosin (25, 50, and 75 mg kg –1 on a dry weight basis) were added to swine manure plus a control, which was composted with cotton stalks. Each treatment was repeated in triplicate and the ARG profiles were determined with different levels of tylosin. The top 35 genera and ARGs profiles were clustered together based on the composting time. Combined composting parameters (temperature, pH, NH 4 + -N, NO 3 -N, and moisture content) accounted for 78.4% of the total variation in the changes in the potential host bacteria. In addition, the selected five composting parameters and six phyla (including 25 potential host bacterial genera) explained 46.9% and 30.7% of the variation in the ARG profiles according to redundancy analysis, respectively. The variations in ARGs during the composting process were mainly affected by the dynamics of potential host bacteria rather than integrons and the selective pressure due to bio-Cu and bio-Zn. [ABSTRACT FROM AUTHOR]

Biological nitrogen fixation is a major pathway in ecosystems. This study investigated the effects of adding Cu at different levels (0, 200, and 2000 mg kg −1 ) on the diazotroph community during swine manure composting. Quantitative PCR and high-throughput sequencing were used to analyze the abundances of diazotrophs and the community composition based on the nifH gene. The nifH gene copy number was relatively high in the early stage of composting and Cu had a significant inhibitory effect on the nifH copy number. Furthermore, Cu decreased the diversity of nifH and changed the microbial community structure in the early stage. The nifH genes from members of Firmicutes and Clostridium were most abundant. Co-occurrence ecological network analysis showed that the Cu treatments affected the co-occurrence patterns of diazotroph communities and reduced the associations between different diazotrophs. Interestingly, Cu may weaken symbiotic diazotrophic interactions and enhance the roles of free-living diazotrophs. [ABSTRACT FROM AUTHOR]

Swine manure is an important reservoir for antibiotic resistance genes (ARGs) but anaerobic co-digestion (AcoD) can potentially reduce the abundance of these ARGs. However, few studies have considered the effects of Chinese medicinal herbal residues (CMHRs) on the variations in ARGs and mobile genetic elements (MGEs) during AcoD. Thus, this study explored the fate of ARGs and MGEs during the AcoD of CMHRs and swine manure. The results showed that CMHRs effectively reduced the abundances of the main ARGs (excluding ermF , qnrA , and tetW ) and four MGEs (by 36.7–96.5%) after AcoD. Redundancy analysis showed that changes in the bacterial community mainly affected the fate of ARGs rather than horizontal gene transfer by MGEs. Network analysis indicated that 17 bacterial genera were possible hosts of ARGs. The results of this study suggest that AcoD with CMHRs could be employed to remove some ARGs and MGEs from swine manure. [ABSTRACT FROM AUTHOR]

[Display omitted] • The fate of phage-mediated ARGs in composting was elucidated for the first time. • Adding 5 % HA most effective at removing ARGs and MGEs. • HA effectively inhibited the proliferation of pathogens carrying ARGs. • Environmental factors drive ARGs by affecting the co-host bacteria of b/pARGs. Phages can promote the spread of antibiotic resistance genes (ARGs) in agricultural environments through transduction. However, studies on phage-mediated ARG profiles during composting have not been performed. This study investigated the effects of adding humic acid (HA) on the abundances of bacteria/phage co-mediated ARGs (b/pARGs) during swine manure composting and the key factors that affected the transmission of b/pARGs. The results showed that the addition of 5 % HA during composting could effectively reduce the absolute abundances of b/pARGs, inhibit the proliferation of pathogenic microorganisms (e.g., Corynebacterium and Streptococcus) that carried ARGs, and ultimately affect the fate of b/pARGs in the composting process by regulating key environmental factors to change the abundance of co-host bacteria. Overall, the findings of this study provided new information for understanding the main driving factors affecting the b/pARGs profile and provided a reference for the prevention and control of ARGs pollution during composting. [ABSTRACT FROM AUTHOR]

The degradation of organic matter (OM) and CH 4 emissions during composting greatly influence the composting efficiency and greenhouse effect. This study evaluated the effects of adding phosphogypsum (PPG) and medical stone (MS) on OM breakdown, CH 4 emissions, and their underlying mechanisms. MS accelerated the breakdown of OM in the early composting stage, whereas PPG increased it in the cooling and maturation periods. At the ending of composting, humification was also significantly promoted by PPG and MS (P < 0.05). Moreover, MS and PPG reduced CH 4 emissions by 27.64% and 23.12%, respectively, and significantly inhibited the activities of methanogens in terms of their abundance (mcrA) and composition (dominant genera such as Methanobrevibacter , Methanocorpusculum , and Methanothermus) (P < 0.05). Interestingly, MS enhanced the activity of enzymes and bacterial metabolism related to OM degradation in the early composting stage, whereas PPG promoted them during the cooling and maturity stages. MS and PPG inhibited the activities of enzymes related to CH 4 release during the cooling and maturity stages. Therefore, PPG and MS may have influenced OM degradation and CH 4 releases during composting via changes in bacterial metabolism and enzyme activity levels. PPG and MS could have altered the activities of methanogens to influence the transformation of carbon and CH 4 emissions according to network analysis and partial least-squares path modeling analysis. These findings provide insights at the molecular level into the effects of adding PPG and MS on OM degradation and CH 4 emissions during composting, thereby facilitating the application of PPG and MS in composting systems. • Phosphogypsum (PPG) and medical stone (MS) added during composting. • MS and PPG altered organic matter (OM) degradation and promoted humification. • MS and PPG reduced CH 4 emissions by 27.64% and 23.13%, respectively. • Activities of enzymes related to OM degradation and CH 4 emissions also assessed. • PPG and MS changed methanogen community to affect carbon conversion and CH 4 release. [ABSTRACT FROM AUTHOR]

[Display omitted] • Adding sepiolite during swine manure composting reduced bioavailability of Cu. • Sepiolite enhanced reductions in the abundances of ARGs and MGEs. • Sepiolite reduced the abundances of genes encoding "drug resistance: antibacterial". • Adding 7.5% sepiolite reduced the abundances of potential host bacteria of ARGs. Manures are storages for antibiotic resistance genes (ARGs) entering the environment. This study investigated the effects of adding sepiolite at 0%, 2.5%, 5%, and 7.5% (CK, T1, T2, and T3, respectively) on the fates of ARGs during composting. The relative abundances (RAs) of the total ARGs in CK and T3 decreased by 0.23 and 0.46 logs, respectively, after composting. The RAs of 10/11 ARGs decreased in CK, whereas they all decreased in T3. The reduction in the RA of the total mobile genetic elements (MGEs) was 1.26 times higher in T3 compared with CK after composting. The bacterial community accounted for 47.93% of the variation in the abundances of ARGs. Network analysis indicated that ARGs and MGEs shared potential host bacteria (PHB), and T3 controlled the transmission of ARGs by reducing the abundances of PHB. Composting with 7.5% sepiolite is an effective strategy for reducing the risk of ARGs proliferating. [ABSTRACT FROM AUTHOR]

[Display omitted] • Kaolin decreased nitrogen loss by reducing the release of NH 3 and N 2 O. • The nosZ expression was upregulated by kaolin while the norB abundance was decreased. • The coexistence of functional genes and MRGs in MAGs was initially elucidated. • Kaolin affected the nitrogen functional genes by passivating heavy metals. The efficient control of nitrogen loss in composting and the enhancement of product quality have become prominent concerns in current research. The positive role of varying concentrations kaolin in reducing nitrogen loss during composting was revealed using metagenomic binning combined with reverse transcription quantitative polymerase chain reaction. The results indicated that the addition of 0.5 % kaolin significantly (P < 0.05) up-regulated the expression of nosZ and nifH on day 35, while concurrently reducing norB abundance, resulting in a reduction of NH 3 and N 2 O emissions by 61.4 % and 17.5 %, respectively. Notably, this study represents the first investigation into the co-occurrence of nitrogen functional genes and heavy metal resistance genes within metagenomic assembly genomes during composting. Emerging evidence indicates that kaolin effectively impedes the binding of Cu/Zn to nirK and nosZ gene reductases through passivation. This study offers a novel approach to enhance compost quality and waste material utilization. [ABSTRACT FROM AUTHOR]

Livestock manure is a major source of antibiotic resistance genes (ARGs) that enter the environment. This study assessed the effects of inoculation with mature compost (MC) on the fates of ARGs and the bacterial community during swine manure composting. The results showed that MC prolonged the thermophilic period and promoted the decomposition of organic matter, which was due to the rapid growth and reproduction of thermophilic bacteria (Bacillus , Thermobifida , and Thermobacillus). MC significantly reduced the relative abundances of ARGs (1.02 logs) and mobile genetic elements (MGEs) (1.70 logs) after composting, especially sulfanilamide resistance genes. The total ARGs removal rate was 1.11 times higher in MC than the control. Redundancy analysis and structural equation modeling showed that horizontal gene transfer mediated by MGEs (IS CR1 and intI1) was the main direct factor related to the changes in ARGs during composting, whereas the C/N ratio and pH were the two most important indirect factors. Network analysis showed that members of Firmicutes comprising Romboutsia , Clostridisensu_stricto_1 , and Terrisporobacter were the main bacterial hosts of ARGs and MGEs. MC reduced the risk of ARGs transmission by decreasing the abundances of bacterial hosts. Thus, MC is a promising strategy for reducing the proliferation risk of ARGs. [Display omitted] • Mature compost increased the abundance of thermophilic bacteria. • Mature compost is an efficient strategy for reducing ARGs and MGEs. • Mature compost decreased ARGs transmission risk by reducing bacterial host. • MGEs (IS CR1 and intI1) were the main direct factors related to changes in ARGs. [ABSTRACT FROM AUTHOR]

This study assessed the effects of superphosphate (SPP) and phosphogypsum (PPG) on the bacterial and fungal community succession and molecular ecological networks during composting. Adding SPP and PPG had positive effects on the bacterial richness and diversity, negative effects on the fungal richness and diversity. The microbial diversity and richness were higher in PPG than SPP. Non-metric multidimensional scaling analysis clearly separated SPP and PPG from the control treatment with no additives. The dominant genera comprised Turicibacter , Bacillus , norank_o_SBR1031 , Thermobifida , norank_f_Limnochordaceae , Truepera , Thermopolyspora, Mycothermus , Dipodascus , Thermomyces , and unclassified_p_Ascomycota. In all treatments, the major bacterial species differed clearly in the later thermophilic, cooling, and maturation composting stages, whereas the main fungal species varied significantly in the thermophilic stage. The changes in the dominant microorganisms in SPP and PPG may have inhibited or promoted the degradation of organic matter during various composting stages. Adding SPP and PPG led to more complex bacterial networks and less complex fungal networks, where SPP had more adverse effects on the fungal networks than PPG. SPP and PPG could potentially alter the co-occurrence patterns of the bacterial and fungal communities by changing the most influential species. SPP and PPG changed the composition and succession of the microbial community by influencing different physiochemical properties during various composting stages where the pH was the main explanatory factor. Overall, this study provides new insights into the effects of SPP and PPG on the microbial community and its interactions during composting. • Superphosphate and phosphogypsum increased the bacterial richness and diversity. • Superphosphate and phosphogypsum affected microbial community succession. • Superphosphate and phosphogypsum changed bacterial and fungal network structures. • pH was the main factor that affected bacterial and fungal communities. • Phosphogypsum had a greater effect on microorganisms than superphosphate. [ABSTRACT FROM AUTHOR]

Green tea residues (GTRs) are byproducts of tea production and processing, and this type of agricultural waste retains nutritious components. This study investigated the co-composting of GTRs with swine manure, as well as the effects of GTRs on antibiotic resistance genes (ARGs) and the bacterial community during co-composting. The temperature and C/N ratio indicate compost was mature after processing. The addition of GTRs effectively promoted the reduction in the abundances of most targeted ARGs (tet and sul genes), mobile genetic element (MGE; intI1), and metal resistance genes (MRGs; pcoA and tcrB). Redundancy analysis (RDA) showed that GTRs can reduce the abundance of MRGs and ARGs by reducing the bioavailability of heavy metals. Network analysis shows that Firmicutes and Actinobacteria were the main hosts of ARGs and ARGs, MGEs, and MRGs shared the same potential host bacteria. Adding GTRs during composting may reduce ARGs transmission through horizontal gene transfer (HGT). GTRs affected the bacterial community, thereby influencing the variations in the ARG profiles and reducing the potential risk associated with the compost product. Image 1 • Co-composting is an effective way to treat green tea residues. • Green tea residues effectively reduce tet and sul genes after co-composting. • Firmicutes and Actinobacteria were the main hosts of ARGs. • Some ARGs, MGEs, and MRGs shared the same potential host bacteria. [ABSTRACT FROM AUTHOR]

[Display omitted] • Two-phase inoculation of PGPR effective in reducing abundances of ARGs (0.26 logs). • PGPR reduced the selective pressure imposed by Cu on readily removed ARGs. • Two-phase inoculation reduced abundances of potentially pathogenic ARG hosts. • Two-phase inoculation inhibited HGT of ARGs by reducing abundance of MGEs. • Two-phase inoculation downregulated expression of functional gene related to ARGs. This study investigated the effects on antibiotic resistance genes (ARGs) and the related mechanisms of different plant growth-promoting rhizobacteria (PGPR) inoculation strategies during composting: no inoculation (CK), inoculation in initial phase (T1), inoculation in cooling phase (T2), and inoculation in both initial and cooling phases (T3). After composting, the total relative abundances (RAs) of ARGs decreased by 0.26 and 0.03 logs under T3 and T2, respectively, but increased by 0.05 and 0.22 logs under T1 and CK. The abundances of eight ARGs were lowest under T3, including some high risk ARGs with clinical importance. Bioavailable Cu significantly affected the readily removed ARGs, and PGPR inoculation decreased the bioavailability of Cu. T3 reduced the abundances of potential pathogen hosts, inhibited horizontal gene transfer by reducing the RAs of mobile gene elements (0.48 logs), and downregulated the expression of genes related to ARG propagation, thereby decreasing the ecological risk of ARGs. [ABSTRACT FROM AUTHOR]

• Nitrite mainly reduced by nirS gene product in early phases of composting. • nxrA gene only detected in the late composting phases when nitrite oxidized. • Bacteria that harbored nirS and nxrA competed in the late composting phases. Nitrite has a key role in nitrogen conversion during composting. In this study, the dynamic changes in the NO 2 – contents, abundances of nirS and nxrA , and the bacteria that harbored these genes were determined during composting. NO 2 – accumulated during the initial composting stage. The nirS gene was abundant throughout composting, whereas the nxrA gene was only abundant in the late composting phases. Ralstonia sp. and Thauera sp. were the dominant denitrifiers that harbored nirS , and Nitrobacter winogradskyi Nb-255 was the dominant nitrifier that harbored nxrA. Structural equation modeling showed that NO 2 – was mainly reduced by nirS in the early phases, and oxidized by nxrA in the late phases, but especially in the maturity phase. Network analysis showed that the dominant bacteria harboring nirS and nxrA were hubs in the modules related to the reduction and oxidation of NO 2 –, and they had competitive relationships during the cooling and maturity phases. [ABSTRACT FROM AUTHOR]