Aerobic composting is an effective way to recycle solid waste. Composting promotes the transformation of degradable organic matter in solid waste into mature manure, precursors of humic substances, by microorganisms widely existed in nature, so as to provide nutrient rich fertilizer for the growth of crops. The community and function of microorganisms play a key role in the successful progress of composting. In recent years, with the vigorous development of molecular biology technology, the succession of microbial community in each stage of composting process has been studied more deeply. Thus, we have a deeper understanding of the metabolic function and functional groups of microorganisms in the composting process. The succession law of microbial community in different stages of composting can be summarized as follows: from mesophilic bacteria and fungi to cellulose decomposing bacteria, then cellulose decomposing bacteria, finally lignin decomposing bacteria. These studies will help us develop microbial additives and improve the efficiency of composting. This paper systematically summarizes the research progress of these molecular biology technologies applied in studies on the microbial community of composting, summarizes the research results of succession changes of microbial community in all stages of composting in recent years, introduces the application of microbial additives in aerobic composting, and prospects the future development of microbial additives.

氨氧化古菌(Ammonia-oxidizing archaea,AOA)被认为是酸性土壤硝化过程的主要微生物类群,但AOA如何适应酸性胁迫并发挥作用一直是研究难点,而ATP酶(ATPase)是能量代谢的关键,其编码基因可能在AOA适应酸性胁迫过程中发生了趋同性演化.据此,本研究针对5个不同种植年限的马尾松人工林酸性土壤(15 a、24 a、45 a、55 a、63 a),通过深度宏基因组测序获得7360亿碱基对,重构AOA氨单加氧酶amoA基因和ATP酶A亚基(ATPase subunit A)基因的系统发育进化谱系,研究AOA适酸的分子机制.结果表明:根据经典的amoA基因系统发育进化分类,所有5个森林土壤中优势AOA主要包括Nitrososphaerales和Ca.Nitrosotaleales两大类群,但Nitrososphaerales类群与中碱性土壤中的AOA古菌亲缘关系更近,与嗜酸的Ca.Nitrosotaleales类群亲缘关系较远,表明amoA基因的系统进化关系不能解释Nitrososphaerales在酸性土壤中的成功定殖.然而,基于ATPase subunit A基因的系统进化分析则发现,所有酸性森林土壤中嗜酸/耐酸氨氧化古菌均含有亲缘关系较近的V-ATPase subunit A基因,表明氨氧化古菌可能通过基因水平转移获得V-ATPase基因适应酸性胁迫环境,较好地解释了氨氧化古菌适应酸性胁迫的生境扩展规律.随林龄的增加,Ca.Nitrosotaleales类群丰度先减少后增加,而Nitrososphaerales类群丰度先增加后减少,速效钾是显著影响AOA群落结构的重要环境因子.这些结果表明,不同种植年限下酸性人工林土壤中氨氧化古菌种群发生了明显的分化,V-ATPase基因水平转移可能是氨氧化古菌适应酸性胁迫的重要机制.

Sewage sludge is one of the major environmental reservoirs of antibiotic resistance genes (ARGs), while its recycling releases abundant ARGs into the agricultural soils. Sludge conditioning treatment, as an indispensable step to improve sludge dewatering, can enhance the dewaterability of sewage sludge and meanwhile attenuate ARGs in sludge compost, but it remains unclear how sludge conditioning treatments impact the ARG profiles in different agricultural soils amended with sludge composts. In the present study, the fates of 18 ARGs and 2 mobile genetic elements (MGEs) in two types of agricultural soils (i.e., red soil and yellow-brown soil) were investigated for 170 days, after the land application of sludge composts derived from different conditioning treatments, including bioleaching and chemical conditioning using Fe[III]/CaO or polyacrylamide (PAM). The results showed that the absolute abundance of total ARGs and MGEs was the lowest in both the red soil and the yellow-brown soil amended with bioleached sludge compost (Day 170), which were only 26.4-76.8% of that in the corresponding soils amended with the compost products of raw, PAM-conditioned, or Fe[III]/CaO-conditioned sludge. Besides, in comparison with other conditioning treatments, the bioleaching conditioning treatment more greatly limited the enrichment of typical sludge-borne ARGs (sul2, aadA1, aadA2-01, aadA2-02, and aadA2-03) and their potential hosts. It was found that the much less enrichment of sludge-borne ARGs achieved by bioleaching conditioning most probably resulted from both the low abundance of ARGs in bioleached sludge compost and the limited growth of bacteria carrying ARGs in the amended agricultural soils. Therefore, bioleaching conditioning is superior to the chemical conditioning using Fe[III]/CaO or PAM in mitigating antibiotic resistance in different agricultural soils amended with sludge composts, which was contributed by the preremoval of ARGs in sludge compost and the potentially limited growth of bacteria carrying ARGs after the land application of sludge compost.

Plastic pollution and antibiotic resistance are two emerging environmental and human health crises today. Although it was revealed that microplastics can serve as vectors for the dissemination of antibiotic resistance, it is still unclear how the nanoplastics influence the horizontal transfer of antibiotic resistance genes (ARGs). Herein, we firstly compared the effect of polystyrene (PS) micro/nanoplastics on the transformation of plasmid-borne ARG, using a transformation model consisting of plasmid pUC19 (ampR ) and Escherichia coli DH5α (recipient). Due to its size effect, PS nanoplastics (10-500 mg/L) significantly enhanced the transformation efficiency (2.8-5.4 folds) and frequency (3.2-8.4 folds) of exogenous ampR into E. coli, while PS microplastics exerted no influence. The detailed mechanisms were found that nanoplastics induced reactive oxygen species (ROS) overproduction, activated SOS response, increased cell membrane permeability and changed the secretion systems, thereby facilitating the uptake of exogenous DNA by bacteria. Moreover, the co-presences of nanoplastics with humic acid or Fe3+ relieved to some extent, but did not completely alleviate the promoting effect of nanoplastics on plasmid transformation. Our findings suggest that the risk of nanoplastics on promoting the dissemination of antibiotic resistance should not be neglected, and further studies are needed to investigate such risk in complex environments.

Sustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant-associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and evaluating changes in ecosystem functions. Here, we leverage a long-term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil-depth gradient in poplar, restored prairie and switchgrass to understand their effects on the microbial communities. High throughput amplicon sequencing of the fungal internal transcribed spacer (ITS) and prokaryotic 16S DNA regions showed a common trend of root and soil microbial community richness decreasing and evenness increasing with depth. Ecological niche (root vs. soil) had the strongest effect on community structure, followed by depth, then crop. Stochastic processes dominated the structuring of fungal communities in deeper soil layers while operational taxonomic units (OTUs) in surface soil layers were more likely to co-occur and to be enriched by plant hosts. Prokaryotic communities were dispersal limited at deeper depths. Microbial networks showed a higher density, connectedness, average degree and module size in deeper soils. We observed a decrease in fungal-fungal links and an increase of bacteria-bacteria links with increasing depth in all crops, particularly in the root microbiome.

The discovery of complete ammonia oxidation (comammox), oxidizing ammonia to nitrate via nitrite in a single organism, has redefined the traditional recognition of the two-step nitrification driven by two functional groups (ammonia-oxidizing and nitrite-oxidizing microorganisms). However, the understanding of the distribution and niche differentiation of comammox Nitrospira in the estuarine mudflats and their reclaimed agricultural soils is still limited. Here, we investigated the abundance, diversity and community structures of comammox Nitrospira in the mudflats and the reclaimed agricultural soils in the northern Yangtze River estuary. Quantitative PCR showed the abundances of amoA genes of comammox were lower than that of ammonia-oxidizing bacteria (AOB) in nearly all samples. Amplicon sequencing of amoA genes revealed that the community structures of comammox Nitrospira were significantly ( P < 0.001) different between the original mudflats and the reclaimed agricultural soils, indicating niche differentiation among comammox Nitrospira clades (clade A.1, clade A.2, and clade B). The clade A.1 was the dominant group of comammox Nitrospira in the mudflats, while clade B predominated in the agricultural soils. However, the members of clade A.2 could be clearly divided into two groups, the mudflat-preferred and agricultural soil-preferred groups, suggesting more complicated ecological preferences within this sub-clade. Furthermore, it was demonstrated that salinity, organic matter (OM) and NO 3 – -N had a significantly influence on the distribution of comammox Nitrospira in the estuarine environment. Clade A.1 and nearly half members of clade A.2 were positively correlated with salinity, and negatively correlated with the concentrations of OM and NO 3 – -N. In contrast, the clade B and the other half members of clade A.2 showed the exact opposite pattern: a negative correlation with salinity and positive correlation with OM and NO 3 – -N. The co-occurrence network demonstrated that the operational taxonomic units (OTUs) within the same (sub-)clade were mostly positively correlated, indicating the similar niche preferences among the members from the same (sub-)clade of comammox Nitrospira . Taken together, our results revealed the niche differentiation of comammox Nitrospira in estuarine ecosystems where salinity and OM were the primary factors responsible for the distinct ecological distribution patterns.

全球30％以上陆地面积是酸性土壤(pH<5.5),而酸性土壤中氨氧化微生物群落特征研究是破译其硝化过程微生物学机理的基础.尤其随着完全硝化微生物(Complete ammonia oxidizer,comammox)的发现,亟需重新认知酸性土壤中氨氧化微生物类群.以酸性马尾松林为研究对象,综合利用荧光定量PCR(qPCR)、凝胶电泳半定量和宏基因组测序等技术研究土壤中氨氧化古菌(Ammonia-oxidizing archaea,AOA)、氨氧化细菌(Ammonia-oxidizing bacteria,AOB)和Comammox的相对丰度以及群落组成特征.研究发现AOA和AOB amoA基因丰度分别为2.61×106 copies·g–1和1.45×106 copies·g–1;而comammox amoA基因qPCR结果存在显著的非特异性扩增,导致其丰度被高估,而经凝胶电泳半定量矫正后,约为(1.38～1.47)×106 copies·g–1,该结果和土壤宏基因测序揭示的comammox相对丰度基本吻合.此外,宏基因组分析发现经典嗜酸group 1.1a-associated仅占AOA总类群的12％,而group 1.1b则占88％,尽管目前仍未有嗜酸group 1.1b AOA纯菌株的报道.AOB主要类群为Nitrosospira(约64％),而Nitrosomonas约占36％.Comammox主要类群为clade B(约64％),而clade A仅占36％且均隶属于clade A.1亚枝,这暗示clade B与已报道的嗜中性comammox clade A纯菌株有极大的生理代谢差异.总之,本研究提供了综合利用qPCR、半定量和宏基因组分析土壤氨氧化微生物群落的策略,并建议优化comammox的qPCR引物,同时本研究系统分析了酸性马尾松林土壤中氨氧化微生物的相对丰度和群落组成特征.

Morels (Morchella spp.) are popular edible fungi with significant economic and scientific value. However, white mold disease, caused by Paecilomyces penicillatus, can reduce morel yield by up to 80% in the main cultivation area in China. Paecilomyces is a polyphyletic genus and the exact phylogenetic placement of P. penicillatus is currently still unclear. Here, we obtained the first high-quality genome sequence of P. penicillatus generated through the single-molecule real-time (SMRT) sequencing platform. The assembled draft genome of P. penicillatus was 40.2 Mb, had an N50 value of 2.6 Mb and encoded 9454 genes. Phylogenetic analysis of single-copy orthologous genes revealed that P. penicillatus is in Hypocreales and closely related to Hypocreaceae, which includes several genera exhibiting a mycoparasitic lifestyle. CAZymes analysis demonstrated that P. penicillatus encodes a large number of fungal cell wall degradation enzymes. We identified many gene clusters involved in the production of secondary metabolites known to exhibit antifungal, antibacterial, or insecticidal activities. We further demonstrated through dual culture assays that P. penicillatus secretes certain soluble compounds that are inhibitory to the mycelial growth of Morchella sextelata. This study provides insights into the correct phylogenetic placement of P. penicillatus and the molecular mechanisms that underlie P. penicillatus pathogenesis.

After the discovery of complete ammonia-oxidizing (comammox) Nitrospira, detection and assessments of the contribution of comammox Nitrospira communities to nitrogen cycling are in great demand. PCR-based approach, a common method for the detection of comammox, depends strongly on accurate amplification of the amoA genes from the original DNA samples using appropriate primers. In this study, we reported an evaluation of the performance of two commonly used primer sets, Ntsp-amoA 162F/359R and comaA/B-244f/659r, for amplifying the comammox amoA genes from three representative wetland soils in China [Sangsang (SS), Sanjiang (SJ), and Xianghai (XH)]. Our results demonstrated the two primer sets could both successfully amplify the clades with high relative abundances (RA), and further revealed a broadly similar diversity and community composition of dominant comammox operational taxonomic units (OTUs) (RA ≥ 1%) in each of the three wetland soils. However, the clades with low RA, such as the clade A (1.26%) in SJ and the clade B (11.54%) in XH that were recovered by metagenomics analysis, failed to be amplified using comaA/B-244f/659r, but were successfully amplified and sequenced using Ntsp-amoA 162F/359R. It indicated that, compared to comaA/B-244f/659r, Ntsp-amoA 162F/359R was more sensitive to the clades with low RA. However, it is worth noting that Ntsp-amoA 162F/359R would overestimate the RA of some rare clades. For example, the RAs of clade B in XH were overestimated by 32-fold. Furthermore, high levels of non-target amplification were detected via gel electrophoresis using both primer sets, especially for comammox Clade B amoA genes, implying that we should treat qPCR results based on these primers with caution. Taken together, our study comprehensively compared the performance of the two primer sets on the sensitivity and specificity of amplifying comammox amoA genes in three wetland soils, pointing out the necessity of further development of new primers for the efficient and accurate detection of comammox in various environments.

Sphaerosporella brunnea is a pioneer ectomycorrhizal fungus with facultative saprophytic capacities. Here, we sequenced the genome of S. brunnea strain Sb_GMNB300, which is estimated at 51.6 Mb in size with 872 assembled contigs accounting for 12,597 predicted coding genes. This genome will be useful for comparative studies of Pezizales ectomycorrhizal symbioses.

Gloeostereum incarnatum is a precious edible mushroom that is widely grown in Asia and known for its useful medicinal properties. Here, we present a high-quality genome of G. incarnatum using the single-molecule real-time (SMRT) sequencing platform. The G. incarnatum genome, which is the first complete genome to be sequenced in the family Cyphellaceae, was 38.67 Mbp, with an N50 of 3.5 Mbp, encoding 15,251 proteins. Based on our phylogenetic analysis, the Cyphellaceae diverged ~174 million years ago. Several genes and gene clusters associated with lignocellulose degradation, secondary metabolites, and polysaccharide biosynthesis were identified in G. incarnatum, and compared with other medicinal mushrooms. In particular, we identified two terpenoid-associated gene clusters, each containing a gene encoding a sesterterpenoid synthase adjacent to a gene encoding a cytochrome P450 enzyme. These clusters might participate in the biosynthesis of incarnal, a known bioactive sesterterpenoid produced by G. incarnatum. Through a transcriptomic analysis comparing the G. incarnatum mycelium and fruiting body, we also demonstrated that the genes associated with terpenoid biosynthesis were generally upregulated in the mycelium, while those associated with polysaccharide biosynthesis were generally upregulated in the fruiting body. This study provides insights into the genetic basis of the medicinal properties of G. incarnatum, laying a framework for future characterization of bioactive proteins and pharmaceutical uses of this fungus.

Dibutyl phthalate (DBP) is a typical soil contaminant that is widely used as plasticizer in modern agricultural production. In this study, an experiment was conducted to evaluate fungal community succession in a soil-vegetable ecosystem under different DBP concentrations. By using high-throughput sequencing of the ribosomal internal transcribed spacer (ITS) region, it was shown that DBP contamination caused significant changes to the soil fungal community, in terms of both α and β diversities. The largest changes in fungal α and β diversities were detected under 50 mg/kg DBP concentration at the first day of addition. The bulk soils, rhizosphere soils and the phyllosphere harbored different fungal communities, while the abundance of saprotrophs and plant pathogens in the phyllosphere have been increased under DBP contamination. From correlation analysis and partial Mantel test, the change in fungal community α diversity was the result of multiple factors (DBP concentration, bacterial community and soil properties) while the β diversity of fungal community was mainly co-varied with the bacterial community after DBP contamination. Moreover, molecular ecological network analysis demonstrated that DBP contamination was detrimental to mutualistic relationships among fungal species and destabilized the network structure. Overall, the fungal communities in soils and around vegetables were largely remolded by DBP contamination that provides new insight into DBP contamination impacts on agricultural ecosystems.

A phthalate esters-degrading bacterial strain, designated QH-11T, was isolated from an activated sludge wastewater treatment plant in Beijing, PR China. The cells were aerobic, Gram-stain-positive, non-motile, catalase-positive, oxidase-negative, short rods and formed white colonies on trypticase soy agar. This isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and whole-cell hydrolysates contained arabinose and ribose. Diphosphatidylglycerol and phosphatidylethanolamine were the predominant polar lipids. According to the results of full-length of 16S rRNA gene sequence analysis, QH-11T represented a member of the genus Gordonia and showed the highest sequence similarity to Gordonia hydrophobica DSM 44015T (99.2 %), but was distinguishable by a low level of DNA-DNA relatedness (37.8 %). Genome-based comparisons indicated a clear distinction from the top ten most similar type strains (16S rRNA gene sequence) with pairwise average nucleotide identities (ANI) between 74.6 and 83.4 %. The predominant respiratory quinone was MK-9(H2), the mycolic acids present had 56 to 62 carbon atoms, and the major fatty acids were C16 : 0 (33.3 %), C17 : 1ω8c (23.4 %) and C18 : 1ω9c (17.9 %). The DNA G+C content was 68.0 mol%. On the basis of the results of DNA-DNA hybridization, ANI and physiological and biochemical tests, it is proposed that QH-11T represents a novel species of the genus Gordonia, for which the name Gordonia phthalatica sp. nov. is proposed. The type strain is QH-11T (CICC 24107T =KCTC 39933T).

With the rapid development of petro-chemical industry as well as the stricter requirement of environmental protection, the treatment of oily sludge is around the corner for the petroleum companies. A pilot experiment had been carried out in this study to investigate the changes of n-alkanes, polycyclic aromatic hydrocarbons and total petroleum hydrocarbons in the oily sludge. Results show that the oil content in the sludge decreased to 5023 mg/kg within 90 days, which provide technical support for the engineering application of bio pile treatment

为了探索钴(Co)对植物根际微生物的毒性效应,以黑麦草作为供试植物,采用Biolog技术测定了钴对黑麦草根际微生物种群的影响,并测试根际微生物对31种碳源的利用情况.结果发现:低浓度钴处理(20 mg/kg和100 mg/kg)促进了根际微生物的活性,培养40d后根际微生物的Biolog板每孔平均颜色变化率显著高于对照组和高浓度(1000 mg/kg)处理组(P＜0.05),高浓度钴处理对根际微生物活性没有明显的促进作用.不同浓度钴处理组黑麦草根际微生物的Shannon-Wiener指数和Simpson指数变化规律表明,低浓度钴处理(20 mg/kg和100 mg/kg)能够提高黑麦草根际微生物种群的系统稳定性.碳源利用结果表明,L-丝氨酸、β-甲基D-葡萄糖苷、D-甘露醇等19种碳源对黑麦草根际微生物作用明显.

Pannonibacter phragmitetus CGMCC9175 is a halotolerant polycyclic aromatic hydrocarbon (PAH)-degrading bacterium isolated from PAH-contaminated intertidal zone sediment. Here, we report the 5.7-Mb draft genome sequence of this strain, which will provide insights into the diversity of Pannonibacter and the mechanism of PAH degradation in sediments.

A bacterial strain QH-12 isolated from activated sludge was identified as Gordonia sp. based on analysis of 16S rRNA gene sequence and was found to be capable of utilizing dibutyl phthalate (DBP) and other common phthalate esters (PAEs) as the sole carbon and energy source. The degradation kinetics of DBP under different concentrations by the strain QH-12 fit well with the modified Gompertz model (R2 > 0.98). However, strain QH-12 could not utilize the major intermediate product phthalate (phthalic acid; PA) as the sole carbon and energy source, and only a little amount of PA was detected. The QH-12 genome analysis revealed the presence of putative hydrolase/esterase genes involved in PAEs-degradation but no phthalic acid catabolic gene cluster was found, suggesting that a novel degradation pathway of PAEs was present in Gordonia sp. QH-12. This information will be valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs-degrading Gordonia sp. strains.

Sphingobium yanoikuyae TJ is a halotolerant di-n-butyl-phthalate-degrading bacterium, isolated from the Haihe estuary in Bohai Bay, Tianjin, China. Here, we report the 5.1-Mb draft genome sequence of this strain, which will provide insights into the diversity of Sphingobium spp. and the mechanism of phthalate ester degradation in the estuary.

Paenibacillus polymyxa strain EBL06 is a plant growth-promoting bacterium with high antifungal activity. The estimated genome of this strain is 5.68 Mb in size and harbors 4,792 coding sequences (CDSs).

Aquamicrobium defluvii W13Z1 was isolated from petroleum-contaminated drill cuttings from the Bohai Sea and could degrade petroleum hydrocarbon with 5% NaCl at 15°C. Here, we present the 4.8-Mb draft genome sequence of this strain, which may provide useful information about the mechanism of petroleum degradation in drill cuttings.