Falsochrobactrum shanghaiense sp. nov., isolated from paddy soil and emended description of the genus Falsochrobactrum.

A non-spore-forming, motile, Gram-stain-negative, short rod-shaped strain, designated HN4T, was isolated from a paddy soil sample collected in Shanghai, China. A comparative analysis o-f 16S rRNA gene sequences showed that strain HN4T fell within the genus Falsochrobactrum, forming a clear cluster with the type strain of Falsochrobactrum ovis, with which it exhibited a 16S rRNA gene sequence similarity value of 98.2 %. Strain HN4T grew optimally at pH 7.0, 30-35 °C and in the presence of 1 % (w/v) NaCl. It was positive for oxidase activity. Chemotaxonomic analysis showed that strain HN4T contained ubiquinone-10 as the predominant respiratory quinone and possessed summed feature 8(C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0cyclo ω8c as predominant fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The DNA G+C content was 56.9 mol%. Strain HN4T exhibited a DNA-DNA relatedness level of 18±1 % with Falsochrobactrum ovis CCM 8460T. Based on the data obtained in this study, strain HN4T represents a novel species of the genus Falsochrobactrum, for which the name Falsochrobactrumshanghaiense sp. nov. is proposed. The type strain is HN4T (=JCM 32785T=CCTCC AB 2018063T).

Construction, properties, and application of the pCB5 plasmid, a novel conjugative shuttle vector with a Cupriavidus basilensis origin of replication.

Cupriavidus basilensis is a species with diverse metabolic capabilities, including degradation of xenobiotics and heavy metal resistance. Although the genomes of several strains of this species have been sequenced, no plasmid has yet been constructed for genetic engineering in this species. In this study, we identified a novel plasmid, designated pWS, from C. basilensis WS with a copy number of 1-3 per cell and a length of 2150 bp. pWS contained three protein-coding genes, among which only rep was required for plasmid replication. Rep showed no homology with known plasmid replication initiators. Unlike most plasmids, pWS did not have a cis-acting replication origin outside the region of rep. The minimal replicon of pWS was stable in C. basilensis WS without selection. A conjugative C. basilensis/Escherichia coli shuttle vector, pCB5, was constructed using the minimal replicon of pWS. Interestingly, the copy number of pCB5 was flexible and could be manipulated. Enhancing the expression level of Rep in pCB5 by either doubling the promoter or coding region of rep resulted in doubling of the plasmid copy number. Moreover, replacing the native promoter of rep with the lac promoter increased the copy number by over fivefold. Finally, using two different ß-galactosidase reporting systems constructed with pCB5, we successfully demonstrated the different regulatory patterns of bph and dmp operons during diphenyl ether (DE) degradation in C. basilensis WS. Thus, this shuttle vector provided an efficient tool for DNA cloning and metabolic engineering in C. basilensis.

The unexpected effect of the compound microbial agent NP-M2 on microbial community dynamics in a nonylphenol-contaminated soil: the self-stability of soil ecosystem.

Background: Nonylphenol (NP) is widely recognized as a crucial environmental endocrine-disrupting chemical and persistent toxic substance. The remediation of NP-contaminated sites primarily relies on biological degradation. Compound microbial products, as opposed to pure strains, possess a greater variety of metabolic pathways and can thrive in a wider range of environmental conditions. This characteristic is believed to facilitate the synergistic degradation of pollutants. Limited research has been conducted to thoroughly examine the potential compatibility of compound microbial agents with indigenous microflora, their ability to function effectively in practical environments, their capacity to enhance the dissipation of NP, and their potential to improve soil physicochemical and biological characteristics. Methods: In order to efficiently eliminate NP in contaminated soil in an eco-friendly manner, a simulation study was conducted to investigate the impact of bioaugmentation using the functional compound microbial agent NP-M2 at varying concentrations (50 and 200 mg/L) on the dynamics of the soil microbial community. The treatments were set as follows: sterilized soil with 50 mg/kg NP (CK50) or 200 mg/kg NP (CK200); non-sterilized soil with 50 mg/kg NP (TU50) or 200 mg/kg NP (TU200); non-sterilized soil with the compound microbial agent NP-M2 at 50 mg/kg NP (J50) or 200 mg/kg NP (J200). Full-length 16S rRNA analysis was performed using the PacBio Sequel II platform. Results: Both the indigenous microbes (TU50 and TU200 treatments) and the application of NP-M2 (J50 and J200 treatments) exhibited rapid NP removal, with removal rates ranging from 93% to 99%. The application of NP-M2 further accelerated the degradation rate of NP for a subtle lag period. Although the different treatments had minimal impacts on the soil bacterial α-diversity, they significantly altered the ß-diversity and composition of the bacterial community. The dominant phyla were Proteobacteria (35.54%-44.14%), Acidobacteria (13.55%-17.07%), Planctomycetes (10.78%-11.42%), Bacteroidetes (5.60%-10.74%), and Actinobacteria (6.44%-8.68%). The core species were Luteitalea_pratensis, Pyrinomonas_methylaliphatogenes, Fimbriiglobus_ruber, Longimicrobium_terrae, and Massilia_sp003590855. The bacterial community structure and taxon distribution in polluted soils were significantly influenced by the activities of soil catalase, sucrase, and polyphenol oxidase, which were identified as the major environmental factors. Notably, the concentration of NP and, to a lesser extent, the compound microbial agent NP-M2 were found to cause major shifts in the bacterial community. This study highlights the importance of conducting bioremediation experiments in conjunction with microbiome assessment to better understand the impact of bioaugmentation/biostimulation on the potential functions of complex microbial communities present in contaminated soils, which is essential for bioremediation success.

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We analyzed the particle size distribution of soil aggregates in 0-20 and 20-40 cm soil layers of rice-wheat rotation field based on a field plot test with two treatments, conventional straw returning (CK) and straw returning with the addition of straw decomposition promoting microbial inoculants (IT). We evaluated the water stability indices of soil aggregates (the number of soil water stable large aggregates R0.25, the average weight diameter MWD, and the geometric average diameter GMD), and measured the contents of soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) in the soil aggregates of ＜0.053, 0.053-0.25, 0.25-1, ＞1 mm. The results showed that: 1) The number of aggregates ＜0.053, 0.053-0.25, ＞0.25 mm in the 0-20 and 20-40 cm soil layers under IT decreased by 10.0% and 6.8%, increased by 3.0% and 5.7%, and 17.9% and 26.1% compared with CK, respectively. IT effectively increased R0.25, MWD, and GMD by 26.4%, 20.0%, 18.2% and 18.2%, 10.5%, 10.0% in 0-20 and 20-40 cm soil, respectively. 2) Compared to CK, the TP content of 0.25-1 mm aggregates in 0-20 and 20-40 cm soil under IT was significantly increased by 40.3% and 37.5%, respectively, without difference in TN and SOC contents. There was no significant difference in nutrient contents of the other aggregates between the treatments. The contents of SOC and TN in large aggregates (>0.25 mm) were higher than those in silty aggregates (<0.053 mm). Compared to CK, the cumulative contribution rates of SOC, TN and TP of <0.053 mm aggregates under IT were decreased in two soil layers. There was no significant difference in the nutrient cumulative contribution rates of 0.053-0.25 mm aggregates between treatments. The cumulative contribution rates of SOC, TN, and TP of large aggregates (>0.25 mm) under IT were 32.1%, 19.6%, 52.8% and 22.8%, 11.8%, 42.9% higher than those under CK in 0-20 and 20-40 cm soils, respectively. 3) The number of <0.053 mm aggregates was significantly negatively correlated with SOC and TP contents, while that of 0.053-0.25 mm aggregates was negatively correlated with nutrient content. The number of large aggregates (>0.25 mm) were significantly positively correlated with SOC, TN, and TP contents. In conclusion, straw returning with microbial-inoculant addition could promote the formation of soil macroaggregates (>0.25 mm), and improve the water stability of soil aggregates, increasing nutrient contents in soil macroaggregates, with the nutrients transferring from silty aggregates to macroaggregates.

γ-Polyglutamic Acid Production, Biocontrol, and Stress Tolerance: Multifunction of Bacillus subtilis A-5 and the Complete Genome Analysis.

Bacillus subtilis A-5 has the capabilities of high-molecular-weight γ-PGA production, antagonism to plant pathogenic fungi, and salt/alkaline tolerance. This multifunctional bacterium has great potential for enhancing soil fertility and plant security in agricultural ecosystem. The genome size of B. subtilis A-5 was 4,190,775 bp, containing 1 Chr and 2 plasmids (pA and pB) with 43.37% guanine-cytosine content and 4605 coding sequences. The γ-PGA synthase gene cluster was predicted to consist of pgsBCA and factor (pgsE). The γ-PGA-degrading enzymes were mainly pgdS, GGT, and cwlO. Nine gene clusters producing secondary metabolite substances, namely, four unknown function gene clusters and five antibiotic synthesis gene clusters (surfactin, fengycin, bacillibactin, subtilosin_A, and bacilysin), were predicted in the genome of B. subtilis A-5 using antiSMASH. In addition, B. subtilis A-5 contained genes related to carbohydrate and protein decomposition, proline synthesis, pyruvate kinase, and stress-resistant proteins. This affords significant insights into the survival and application of B. subtilis A-5 in adverse agricultural environmental conditions.

Effects of Bacillus subtilis A-5 and its fermented γ-polyglutamic acid on the rhizosphere bacterial community of Chinese cabbage.

Chemical fertilizer reduction combined with novel and green agricultural inputs has become an important practice to improve microecological health in agricultural production. Given the close linkages between rhizosphere processes and plant nutrition and productivity, understanding how fertilization impacts this critical zone is highly important for optimizing plant-soil interactions and crop fitness for agricultural sustainability. Here, by using a pot experimental system, we demonstrated that nitrogen fertilizer reduction and microbial agent application promoted plant fitness and altered the microbial community structure in the rhizosphere soil with the following treatments: no fertilization, CK; conventional chemical fertilizer, CF; 30% reduced nitrogen fertilizer, N; 30% reduced nitrogen fertilizer with pure γ-PGA, PGA; 30% reduced nitrogen fertilizer with Bacillus subtilis A-5, A5; 30% reduced nitrogen fertilizer with γ-PGA fermentation broth, FJY. The PGA, A5, and FJY treatments all significantly promoted crop growth, and the FJY treatment showed the strongest positive effect on Chinese cabbage yield (26,385.09 kg/hm2) (P < 0.05). Microbial agents affected the α diversity of the rhizosphere bacterial community; the addition of B. subtilis A-5 (A5 and FJY treatments) significantly affected rhizospheric bacterial community structure. Urease activity and soil pH were the key factors affecting bacterial community structure and composition. The FJY treatment seemed to influence the relative abundances of important bacterial taxa related to metabolite degradation, predation, and nitrogen cycling. This discovery provides insight into the mechanism underlying the effects of microbial agent inputs on rhizosphere microbial community assembly and highlights a promising direction for the manipulation of the rhizosphere microbiome to yield beneficial outcomes.

Using Mathematical Models to Study the Influences of Different Ratios of Chemical Nitrogen, Phosphorus, and Potassium on the Content of Soluble Protein, Vitamin C, and Soluble Sugar in Melon.

The current fertilizer recommendations for melon plantation have many limitations and exhibit deficiencies regarding future development. Therefore, in this study, the optimal quantities of fertilizer, in terms of the effects of single factors and interaction effects, are studied. There were significant interaction effects between N and P, N and K, P and K; the contents of soluble protein, vitamin C (Vc), and soluble sugar in melon could be improved using the optimal fertilization ratios. The optimal ratio of N:P:K was 2.33:1:3.85, with the amounts of N, P2O5, and K2O, respectively, being 157.5, 67.58, and 260.38 kg/hm2, yielding 8.73 g/kg of soluble protein in melon. The optimal ratio of N:P:K was 2.03:1:3.36, with amounts of N, P2O5, and K2O being 157.50, 77.40, and 260.38 kg/hm2, respectively, yielding 25.32 g/kg Vc content in melon. Finally, the optimal ratio of N:P:K was 1.53:1:3.36, with the amounts of N, P2O5, and K2O being 118.07, 77.40, respectively, and 260.38 kg/hm2, yielding 13.34% soluble sugar content in melon.

Straw return promoted the simultaneous elimination of sulfamethoxazole and related antibiotic resistance genes in the paddy soil.

Straw return could provide a natural available carbon source for the soil microorganisms, which might affect the environmental behaviours of organic pollutants. In this study, microcosm system was constructed to investigate the effect of rice straw return on the fate of sulfamethoxazole (SMX) and related antibiotic resistance genes (ARGs). The results showed that straw return (1% of soil dry mass) could accelerate the degradation of SMX via co-metabolism. In the treatment group with rice straw, SMX was rapidly decomposed into small molecular compounds (e.g., (Z)-1-amino-3-oxobut-1-en-1-aminium and benzenesulfinic acid) within the first six days, and SMX was undetectable after 60 days; while for the SMX group without rice straw, 1.3 mg kg-1 of SMX still remained at the 60th day. Straw return could enhance the relative abundances of Proteobacteria involved in SMX degradation, including Microvirga and Ramlibacter, which co-metabolized SMX via the degradation pathways of mineralizable components and aromatic compound. Furthermore, straw return significantly eliminated the ARGs. After 60 days, the int1 and sul1 abundances of the treatment group with rice straw were less than one-tenth of the SMX group without rice straw. The redundancy and network analysis of bacterial community and environmental factors showed that dissolved organic carbon and bacteria belonged to Proteobacteria and Actinobacteria might play positive roles in eliminating ARGs. Our results demonstrate that straw return could promote the simultaneous elimination of SMX and corresponding ARGs, which provides a promising approach to effectively treat antibiotics and ARGs in the farmland.

Effects of straw returning combined with earthworm addition on nitrification and ammonia oxidizers in paddy soil.

Introduction: Soil ammonia oxidation, which acts as the first and rate-limiting step of nitrification, is driven by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and complete ammonia oxidizer (comammox, amoA gene of clade-A and clade-B). Straw returning, widely used ecological technology in China, is an effective measure for promoting straw decomposition and soil nutrient cycling when combined with earthworm addition. However, the effects of straw returning combined with earthworm addition on soil ammonia oxidizers remain poorly understood. Methods: A 2-year plot experiment was conducted with 5 treatments: no fertilizer (CK); regular fertilization (RT); straw returning (SR); earthworm addition (W); straw returning + earthworm addition (SRW). The AOA, AOB, comammox clade-A and clade-B community microbial diversities and structures were investigated by high-throughput sequencing. Results: The results showed that (1) compared to RT treatment, W, SR, and SRW treatments all significantly increased the richness of AOA and comammox clade-A and clade-B (p < 0.05), and the richness of AOB was only significantly promoted by SRW treatment (p < 0.05). However, only SRW had a higher comammox clade-B diversity index than RT. (2) The ammonia oxidizer community structures were altered by both straw returning and earthworm addition. Soil NH4 +-N was the critical environmental driver for altering the ammonia oxidizer community structure. (3) Compared with RT treatment, the soil potential nitrification rate (PNR) of W and SRW treatments increased by 1.19 and 1.20 times, respectively. The PNR was significantly positively correlated with AOB abundance (path coefficient = 0.712, p < 0.05) and negatively correlated with clade-B abundance (path coefficient = -0.106, p < 0.05). Discussion: This study provides scientific support for the application of straw returning combined with earthworm addition to improve soil nitrification with respect to soil ammonia-oxidizing microorganisms.

Effects of Biogas Slurry Combined With Chemical Fertilizer on Soil Bacterial and Fungal Community Composition in a Paddy Field.

The application of biogas slurry and chemical fertilizer in paddy fields can be a practical method to reduce the environmental risk and utilize the nutrients of biogas slurry. The responses of bacterial and fungal communities to the application of biogas slurry and chemical fertilizer are important reflections of the quality of the ecological environment. In this study, based on a 3-year field experiment with different ratios of biogas slurry and chemical fertilizer (applying the same pure nitrogen amount), the Illumina MiSeq platform was used to investigate the bacterial and fungal community diversity and composition in paddy soil. Our results revealed that compared with the observations under regular chemical fertilization, on the basis of stable paddy yield, the application of biogas slurry combined with chemical fertilizer significantly enhanced the soil nutrient availability and bacterial community diversity and reduced the fungal community diversity. Dissolved organic carbon (DOC), DOC/SOC (soil organic carbon), available nitrogen (AN) and available phosphorus (AP) were positively correlated with the bacterial community diversity, but no soil property was significantly associated with the fungal community. The bacterial community was primarily driven by the application of biogas slurry combined with chemical fertilizer (40.78%), while the fungal community was almost equally affected by the addition of pure biogas slurry, chemical fertilizer and biogas slurry combined with chemical fertilizer (25.65-28.72%). Biogas slurry combined with chemical fertilizer significantly enriched Proteobacteria, Acidobacteria, Planctomycetes, Rokubacteria, and Ascomycota and depleted Chloroflexi, Bacteroidetes, Crenarchaeota, Basidiomycota, and Glomeromycota. The observation of the alteration of some bacteria- and fungus-specific taxa provides insights for the proper application of biogas slurry combined with chemical fertilizer, which has the potential to promote crop growth and inhibit pathogens.

Effects of long-term integrated agri-aquaculture on the soil fungal community structure and function in vegetable fields.

The diversity and community structure of soil fungi play an important role in crop production and ecosystem balance, especially in paddy-upland vegetable field systems. High-throughput sequencing was used to study changes in the soil fungal community structure and function in paddy-upland vegetable field systems. The results showed that compared with traditional planting, the diversity and community structure of soil fungi were changed by the combination of flooding and drought, the Shannon index increased by 11.07%, and the proportion of the dominant species, Mortierella, decreased by 22.74%. Soil available nitrogen, total phosphorus, available phosphorus, total nitrogen and organic matter played a leading role in the initial stage of the experiment, while the dominant factor changed to total potassium 3 years later and then to soil pH and water content 6 years later. FUNGuild analysis showed that the proportion of three independent trophic modes of soil fungi were increased by the combined flooded-drought model, and there were multiple interaction factors, For example, nutrient supply, pH and planting pattern. This study showed that soil fertility, crop yield and economic benefits were better than the traditional model after three years of planting and breeding. The longer the time, the better the effect.

Differences in kinetic metabolomics in Eisenia fetida under single and dual exposure of imidacloprid and dinotefuran at environmentally relevant concentrations.

Metabolomic responses of earthworms to neonicotinoids are important for understanding their molecular-level toxicity and assessing their ecological risks, but little is known until now. We investigated impact of imidacloprid (IMI, 52.6 ng/g) and dinotefuran (DIN, 52.5 ng/g) on Eisenia fetida metabolomics under single- and dual-compound exposure scenarios for one to four weeks. Dissimilar metabolites and anti-stress strategies were found for different neonicotinoids and exposure scenarios. Specifically, IMI exposure first increased myo-inositol and UDP-glucuronate associated with transmembrane absorption and transformation to IMI-urea, and then increased glutathione and fourteen amino acids (TCA cycle precursors) to resist stress and replenish energy. In contrast, worms exposed to DIN first prepared TCA cycle intermediates from glucosamine-6-phosphate and amino acids, suppressed urea cycle and DIN transformation, and then alleviated oxidative stress by increasing carnosine, nicotinate-D-ribonucleotide and nicotinamide-ß-riboside. Dual exposure increased four eicosanoids by 1.6-1.9-fold, possibly associated with membrane lipid peroxidation; the amino acids consumed to balance the energy metabolism exhibited a wave-like pattern. This study first systematically revealed the compound/time/exposure scenario- dependent effects of trace neonicotinoids on earthworm metabolomics and advanced the understanding of their action modes. Neonicotinoid transformation was closely related to worms' metabolic profiles, providing important insights in contaminant fate in soil ecosystems.

Stochastic processes drive bacterial and fungal community assembly in sustainable intensive agricultural soils of Shanghai, China.

Sustainable intensive cropping systems have been implemented for three decades in suburban agricultural districts of Shanghai, China. These human-managed soils have been developed from paleosol or alluvial soils across different regions. However, little is known about the geographical distribution patterns of microbes and microbial community assembly in the sustainable intensive soils after decades of anthropogenic disturbances. Here, we investigated the impact of local geochemical properties and geographic distance on stochastic/deterministic microbial community assembly processes using high-throughput sequencing and phylogenetic null modeling analysis. Our results showed that soil pH was the most important environmental factor determining bacterial and fungal community structure. Importantly, only soil organic matter was positively correlated with fungal α-diversity, suggesting the efficient use of carbon substrates in sustainable agricultural systems, compensating for the lack of chemical fertilization and reduced tillage in these systems. Both bacterial and fungal communities had robust distance-decay patterns, but the rate of turnover of bacterial taxa was faster than that of fungi. Variation in bacterial and fungal communities was mostly attributed to the simultaneous effects of environmental variables and spatial factors. We also mapped the spatial distributions of the dominant bacterial and fungal taxa across the sustainable agricultural fields, making it possible to forecast the responses of agricultural ecosystems to anthropogenic disturbance. Based on the patterns of the ß-nearest taxon index, this study demonstrated that stochastic processes shaped substantial bacterial and fungal community variation in sustainable intensive agricultural soils of the Shanghai suburbs. This variation may be attributed to the increasing microbial dispersal caused by hydrological connectivity in the agricultural fields or the release from environmental stress and weakened environmental filtering across the suitable pH range preferable for most soil microbes. These results unveil assembly mechanisms of soil microbial community after several decades of sustainable intensive management, and contribute to understand the role of microbes in ecosystems in establishing a functional equilibrium which may enable sustainability to be preserved.

Efficient biodegradation of DEHP by CM9 consortium and shifts in the bacterial community structure during bioremediation of contaminated soil.

Di(2-ethylhexyl) phthalate (DEHP), the most extensively used plasticizer in plastic formulations, is categorized as a priority environmental contaminant with carcinogenic, teratogenic, and mutagenic toxicities. Many isolated microorganisms exhibit outstanding performance as pure cultures in the laboratory but are unable to cope with harsh environmental conditions in the field. In the present study, a microbial consortium (CM9) with efficient functionality was isolated from contaminated farmland soil. CM9 could consistently degrade 94.85% and 100.00% of DEHP (1000 mg/L) within 24 h and 72 h, respectively, a higher efficiency than those of other reported pure and mixed microorganism cultures. The degradation efficiencies of DEHP and di-n-butyl phthalate were significantly higher than those of dimethyl phthalate and diethyl phthalate (p < 0.05). The primary members of the CM9 consortium were identified as Rhodococcus, Niabella, Sphingopyxis, Achromobacter, Tahibacter, and Xenophilus. The degradation pathway was hypothesized to include both de-esterification and ß-oxidation. In contaminated soil, bioaugmentation with CM9 and biochar markedly enhanced the DEHP removal rate to 87.53% within 42 d, compared to that observed by the indigenous microbes (49.31%) (p < 0.05). During simulated bioaugmentation, the dominant genera in the CM9 consortium changed significantly over time, indicating their high adaptability to soil conditions and contribution to DEHP degradation. Rhodococcus, Pigmentiphaga and Sphingopyxis sharply decreased, whereas Tahibacter, Terrimonas, Niabella, Unclassified_f_Caulobacteraceae, and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium showed considerable increases. These results provide a theoretical framework for the development of in situ bioremediation of phthalate (PAE)-contaminated soil by composite microbial inocula.

Long-term effects of straw return and straw-derived biochar amendment on bacterial communities in soil aggregates.

Improving soil structure, fertility, and production is of major concern for establishing sustainable agroecosystems. Further research is needed to evaluate whether different methods of straw returning determine the variations of soil aggregation and the microbial community in aggregates in the long term. In this study, we comparatively investigated the effects of long-term fertilization regimes performed over six years, namely, non-fertilization (CK), chemical fertilization (CF), continuous straw return (CS), and continuous straw-derived biochar amendment (CB), on soil aggregation and bacterial communities in rice-wheat rotation systems. The results showed that straw/biochar application increased soil nutrient content and soil aggregate size distribution and stability at both 0-20 cm and 20-40 cm soil depths, compared with those of CF and CK; CB performed better than CS. CB increased bacterial community diversity and richness in 0-20 cm soil, and evenness in 0-40 cm soil (p < 0.05); CS had no significant effect on these aspects. Variations in the relative abundance of Actinobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, Gemmatimonadetes, and Latescibacteria in specific aggregates confirmed the different effects of straw/biochar on bacterial community structure. The partial least squares discrimination analysis and permutation multivariate analysis of variance revealed that fertilization, aggregate size fractions, and soil depth affected the bacterial community, although their effects differed. This study suggests that CB may reduce chemical fertilizer usage and improve the sustainability of rice-wheat cropping systems over the long term, with a better overall outcome than CS.

Responses of Soil Bacterial and Fungal Communities to Organic and Conventional Farming Systems in East China.

Organic farming is considered an effective form of sustainable agricultural management. However, understanding of soil microbial diversity and composition under long-term organic and conventional farming is still limited and controversial. In this study, the Illumina MiSeq platform was applied to investigate the responses of soil bacterial and fungal diversity and compositions to organic farming (OF) and improved conventional farming (CF, applied straw retention) in the rice-wheat rotation system. The results highlighted that the alpha diversity of microbial communities did not differ significantly, except for higher bacterial diversity under OF. However, there were significant differences in the compositions of the soil bacterial and fungal communities between organic and conventional farming. Under our experimental conditions, through the ecological functional analysis of significant different or unique bacterial and fungal taxonomic members at the phyla and genus level, OF enhanced nitrogen, sulfur, phosphorus and carbon dynamic cycling in soil with the presence of Nodosilinea, Nitrospira, LCP-6, HB118, Lyngbya, GOUTA19, Mesorhizobium, Sandaracinobacter, Syntrophobacter and Sphingosinicella, and has the potential to strengthen soil metabolic ability with Novosphingobium. On the other hand, CF increased the intensity of nitrogen cycling with Ardenscatena, KD1-23, Iamia, Nitrosovibrio and Devosia, but enriched several pathogen fungal members, including Coniochaeta, Corallomycetella, Cyclaneusma, Cystostereum, Fistulina, Curvularia and Dissoconium.

Characterization of the Propham Biodegradation Pathway in Starkeya sp. Strain YW6 and Cloning of a Novel Amidase Gene mmH.

We previously isolated a monocrotophos-degrading strain Starkeya sp. YW6, which could also degrade propham. Here, we show that strain YW6 metabolizes propham via a pathway in which propham is initially hydrolyzed to aniline and then converted to catechol, which is then oxidized via an ortho-cleavage pathway. The novel amidase gene mmH was cloned from strain YW6 and expressed in Escherichia coli BL21(DE3). MmH, which exhibits aryl acylamidase activity, was purified for enzymatic analysis. Bioinformatic analysis confirmed that MmH belongs to the amidase signature (AS) enzyme family and shares 26-50% identity with several AS family members. MmH (molecular mass of 53 kDa) was most active at 40 °C and pH 8.0 and showed high activity toward propham, with Kcat and Km values of 33.4 s-1 and 16.9 µM, respectively. These characteristics make MmH suitable for novel amide biosynthesis and environmental remediation.

Effect of Straw and Straw Biochar on the Community Structure and Diversity of Ammonia-oxidizing Bacteria and Archaea in Rice-wheat Rotation Ecosystems.

Ammonia oxidation is the first and rate-limiting step of nitrification, driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Straw and straw biochar retention are the popular ways to utilize the agricultural by-products in China, but their long-term effects on AOB and AOA still remain poorly understood. Based on a 7-year plot experiment, which had 4 fertilization regimes: no fertilizer (CK), regular fertilization (RT), straw retention (SR) and straw biochar retention (SB), the abundance and the composition of AOB and AOA was investigated before both the harvest of rice and wheat season by quantitative PCR and 454 high-throughput pyrosequencing, respectively. (1) Compared to RT, straw and straw biochar increased AOB abundance and diversity significantly only in wheat season (P < 0.05), and they both ranked as SB > SR > RT. Among fertilized treatments, a significant difference between SR and RT was found in AOB community composition of the winter season (R value = 0.58, P value = 0.02); (2) In contrast, AOA was almost not responsive to organic addition, except the significant enhancement of abundance by biochar in wheat season; (3) After straw and straw biochar addition, soil potential nitrification rates (PNR) was positive correlated to AOB abundance in both rice and wheat season (P < 0.01), not to AOA abundance (P = 0.211 and 0.068, respectively). This study provides scientific support for the potential of straw utilization to improve nitrification in rice-wheat rotation system with respect to soil ammonia oxidation microorganism.

Long-term effects of straw and straw-derived biochar on soil aggregation and fungal community in a rice-wheat rotation system.

BACKGROUND: Soil aggregation is fundamental for soil functioning and agricultural productivity. Aggregate formation depends on microbial activity influencing the production of exudates and hyphae, which in turn act as binding materials. Fungi are also important for improving soil quality and promoting plant growth in a symbiotic manner. There is a scarcity of findings comparing the long-term impacts of different yearly double-crop straw return modes (e.g., straw return to the field and straw-derived biochar return to the field) on soil aggregation and fungal community structure in rice-wheat rotation systems. METHODS: The effects of 6-year continuous straw and straw-derived biochar amendment on soil physicochemical properties and the fungal community were evaluated in an intensively managed crop rotation system (rice-wheat). Soil samples of different aggregates (macroaggregates, microaggregates, and silt clay) from four different fertilization regimes (control, CK; traditional inorganic fertilization, CF; straw returned to field, CS; straw-derived biochar addition, CB) were obtained, and Illumina MiSeq sequencing analysis of the fungal internal transcribed spacer gene was performed. RESULTS: Compared to CF, CS and CB enhanced soil organic carbon, total nitrogen, and aggregation in 0-20 and 20-40 cm soil, with CB exhibiting a stronger effect. Additionally, agrowaste addition increased the mean weight diameter and the geometric diameter and decreased the fractal dimension (p < 0.05). Principal coordinates analysis indicated that fertilization management affected fungal community structure and aggregation distribution. In addition, CS increased fungal community richness and diversity, compared to CK, CB decreased these aspects. Ascomycota, unclassified_k_Fungi, and Basidiomycota were the dominant phyla in all soil samples. At the genus level, CB clearly increased fungi decomposing biosolids (Articulospora in macroaggregates in 0-20 cm soil and Neurospora in macroaggregates in 20-40 cm soil); decreased pathogenic fungi (Monographella in macroaggregates and Gibberella in microaggregates in 0-20 cm soil) and CO2-emission-related fungi (Pyrenochaetopsis in microaggregates and silt clay in 0-40 cm soil) (p < 0.05). Straw and biochar with inorganic fertilizer counteracted some of the adverse effects of the inorganic fertilizer with biochar showing better effects than straw.

Degradation of nonylphenol polyethoxylates by functionalized Fe3O4 nanoparticle-immobilized Sphingomonas sp. Y2.

In this study, the efficiency of the nonylphenol polyethoxylates (NPEOs)-degrading bacterium Sphingomonas sp. strain Y2 was evaluated, which was immobilized by a novel system composed of polydopamine (PD)-coated Fe3O4 iron nanoparticles (IONPs). The PD-IONPs, with a distinct core-shell structure, relatively uniform size, and high saturation magnetization, were prepared for Y2 immobilization. The performance of Y2 was unaffected by this novel immobilization method, exhibiting 79.5% and 99.9% of NPEOs (500ppm) degradation efficiency at day 1 and 2, respectively. Furthermore, separation and recycling were more readily achieved for immobilized cells as compared to free cells. Immobilized cells retained over 70% of the original degradation activity after 6cycles of utilization. These results suggest that Y2-PD-IONPs can be potentially used for NPEOs-contaminated wastewater bioremediation. CAPSULE: Immobilization of Sphingomonas sp. Y2 by functionalized PD-IONPs with easy separation, recycling utilization and high efficiency.