Ottowia caeni sp. nov., a novel phenylacetic acid degrading bacterium isolated from sludge.

A novel bacterium, designated BD-1T, was isolated from a sludge sample. Cells of the novel Gram-stain-negative strain were identified to be facultative anaerobic, non-motile and short rod-shaped. Growth occurred at 15-37 °C (optimum, 30 °C), pH 5.0-10.0 (pH 7.0) and in 0-4.0  % NaCl (2.0 %, w/v). The 16S rRNA gene sequence of strain BD-1T showed the highest sequence similarity to Ottowia thiooxydans DSM 14619T (97.0 %), followed by Ottowia pentelensis DSM 21699T (96.3 %) and less than 96 % to other related strains. The phylogenetic trees revealed that strain BD-1T clustered within the genus Ottowia. Summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c, 48.2 %), C16 : 0 (23.2 %) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c, 8.6 %) were the major fatty acids (>5 %), and ubiquinone-8 was the respiratory quinone. Phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylglycerol were identified as the major polar lipids. Meanwhile, the G+C content of the DNA was 63.6 mol% based on the draft genome analysis. The average nucleotide identity and digital DNA-DNA hybridization values between strain BD-1T and DSM 14619T were 74.5 and 21.4  %, respectively. In addition, the novel strain completely degraded 500 mg l-1 phenylacetic acid within 72 h under the condition of 3 % NaCl. Given the results of genomic, phylogenetic, phenotypic and chemotaxonomic analyses, strain BD-1T was considered to represent a novel species of the genus Ottowia, for which the name Ottowia caeni sp. nov. is proposed. The strain is a potential resource for the bioremediation of phenylacetic acid contaminated water. The type strain is BD-1T (=CGMCC 1.18541T=KCTC 82183T).

[Polyamine-producing Bacteria Regulated the Community Structure of Rhizosphere Bacteria and Reduced the Absorption of Cd in Wheat].

Some functional microorganisms in the soil immobilize heavy metals by adsorption and precipitation, prevent the absorption of heavy metals by crops, and play an important role in the passivation and remediation of medium and mild heavy metal-contaminated soil. A pot experiment was conducted to study the effects of the exogenous polyamine-producing bacterium Bacillus sp. N3 on Cd uptake and the bacterial community composition and function in the rhizosphere soil. The results showed that strain N3 significantly reduced the contents of Cd (64.7%) in wheat grain and DTPA-Cd (50.1%) in rhizosphere soil and increased the pH (from 6.84 to 6.97) and polyamine content. High-throughput sequencing results showed that inoculation of strain N3 reduced the diversity of the bacterial community; however, it increased the relative abundances of ß-Proteobacteria, Bacteroidetes, and Firmicutes in wheat rhizosphere soil. Meanwhile, strain N3 also increased the relative abundances of heavy metal-immobilizing bacteria and plant growth-promoting bacteria (Bacillus, Arthrobacter, Brevundimonas, Ensifer, Pedobacter, Rhizobium, Pseudomonas, Enterobacter, and Serratia) in wheat rhizosphere soil. The PICRUSt function prediction showed that strain N3 increased the copy number of genes involved in antioxidant capacity, hormone synthesis, and sulfur metabolism in wheat rhizosphere soil. These results indicated that the polyamine-producing bacteria N3 reduced the DTPA-Cd content by increasing the pH; the polyamine contents; the abundances of bacteria with heavy metal-immobilizing or plant growth-promoting traits; and the metabolic pathway involved in antioxidant capacity, hormone synthesis, and sulfur metabolism in wheat rhizosphere soil, thus inhibiting the absorption of Cd by wheat. The results provide theoretical basis and technical support for restoring farmland with excessive heavy metals and ensuring the safe production of wheat.

[High-Throughput Sequencing Combined with Metabonomics to Analyze the Effect of Heavy Metal Contamination on Farmland Soil Microbial Community and Function].

Heavy metal contamination affects microbial composition and diversity. The interaction between heavy metal contamination and soil microorganisms has been a hot topic in ecological research. Battery manufacturing has been going on for over six decades in Xinxiang City, resulting in severe soil heavy metal contamination due to battery wastewater runoff. Few studies have investigated the effect of heavy metal contamination due to long-term battery wastewater runoff on microbial diversity and metabolomics in Xinxiang City. In this study, we collected samples from three heavy metal contaminated sites in Xinxiang City and found that Cd and Pb exceeded the recommended thresholds by 34-66 fold and 1.5-2.32 fold, respectively. High-throughput sequencing showed that Bacillus, Arthrobacter, Sphingomonas, and Streptomyces were the dominant bacteria genera, while Olpidium, Plectosphaerella, and Gibellulopsis were the dominant fungi genera, indicating that heavy metal contaminated soil in Xinxiang City was rich in heavy metal tolerant bacteria and fungi due to the long-term heavy metal stress. Correlation analysis showed that total Cu, DTPA extract Cu, and water soluble Pb were significant factors in bacterial diversity, while total Cd, total Ni, total Pb, total Zn, DTPA extract Cu, and water soluble Pb were significant factors in fungal diversity. To better understand the effect of heavy metal contamination on the metabolism of soil microorganisms, we conducted non-targeted metabolomic profiling, which showed significant differences in metabolites across the samples. Pathway enrichment analysis showed that these differential metabolites were involved in pathways such as metabolism, environmental information processing, and genetic Information Processing, which may play a role in heavy metal stress mitigation and environmental adaptation.

[Functional Stability and Applicability of Heavy Metal Passivators in Reducing Cd Uptake by Lettuce].

The use of heavy metal passivators to prevent vegetables from absorbing heavy metals is an important measure to control heavy metal-polluted vegetable fields and to ensure the safe production of vegetables. A pot experiment of planting three times in succession was conducted to study the effects of Bacillus megaterium N3 (N3), rice husk biochar (BC), sheep manure organic fertilizer (SM), strain N3 combined with biochar (BC+N3), and strain N3 combined with sheep manure (SM+N3) on Cd uptake and the functional stability of lettuce using a heavy metal passivator only at the first planting. The comprehensive applicability of the passivation materials was evaluated by the dynamic weighted comprehensive function. The results showed that when lettuce was planted for the first time, compared with the control, all the heavy metal passivators could significantly reduce (61.2%-81%) the Cd content in the edible part of the lettuce. However, in the third cultivation of lettuce, only SM+N3 could significantly reduce the Cd uptake by lettuce, which indicated that SM+N3 had the best functional stability. The dynamic weighted comprehensive function was used to evaluate the Cd content in the edible part of fresh lettuce, available Cd content in the soil, yield, and remediation cost. The results showed that the comprehensive applicability of SM+N3 was the best, followed by that of SM, BC+N3, and BC, and the comprehensive evaluation effect of strain N3 was the worst. The results of this study provide a theoretical basis and technical support for remediation of heavy metal-contaminated vegetable fields.

[Effect of Miscanthus planting on the structure and function of soil bacterial community.] / 芒草种植对土壤细菌群落结构和功能的影响.

Miscanthus is a promising candidate species of second-generation energy crops. To our knowledge, the composition and function of Miscanthus rhizosphere bacterial communities has not yet been reported. In this study, rhizosphere soil samples were collected from Miscanthus (Xiangzamang No. 1) which was grown in Nanyang City for five years and bareground (as the control) to analyze the bacterial community structure and diversity using 16S rRNA gene sequencing on the Illumina MiSeq platform. PICRUSt was used to determine the metabolic and functional abilities of soil bacterial communities. Phylogenetic analysis based on 16S rRNA gene sequences showed that sol bacteria could be divided into 23 phyla and 231 genera, with high richness of the community composition. The dominant phyla were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Bacteroidetes and Gemmatimonadetes. The bacterial community diversity in the rhizosphere samples of Xiangzamang No. 1 was lower than that in unplanted samples. Rhizosphere bacterial communities were affected by Miscanthus crops. Based on the PICRUSt analysis of bacterial community functions, our results revealed a wide genetic diversity of organisms involved in various essential processes,such as amino acid transport and metabolism, cell wall/membrane/envelope biogenesis, signal transduction mechanisms. Based on the 16S rRNA gene copy number of the detected phylotypes, 22 bacterial metabolic function in the rhizosphere samples of Miscanthus was higher than that in bareground. Results from N- and P-cycling gene analysis showed that Miscanthus planting altered the N- and P-cycling metabolic capacities of soil bacteria.

[Community Structure and Predictive Functional Analysis of Surface Water Bacterioplankton in the Danjiangkou Reservoir].

Bacterioplankton are important components of aquatic ecosystems, and play a crucial role in the global biogeochemical cycle of nitrogen. In this study, surface-water samples were collected from Kuxin (the center of Danjiangkou Reservoir) and Qushou (the Middle Route of the South-to-North Water Diversion Project's canal head) in the Danjiangkou Reservoir in May 2016. Total DNA was isolated, and high-throughput sequencing was performed to analyze the community structure and diversity of bacteria. Phylogenetic analyses of 16S rDNA sequences showed that bacterial communities included species from 12 major phylogenetic groups. The predominant phylogenetic groups included Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, and Verrucomicrobia. The microbial biodiversity of Danjiangkou Reservoir bacterioplankton was greater in water samples from Qushou than in those from Kuxin. PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) was used to determine the metabolic and functional abilities of the observed bacterial communities. Our results revealed a wide genetic diversity of organisms involved in various essential processes, such as Amino acid transport and metabolism, Transcription, Energy production and conversion, and Carbohydrate transport and metabolism. Thirty-five metabolic pathways involving nitrogen were detected. Key genes impacting the nitrogen cycle were detected in both the Kuxin and Qushou samples, and these encoded enzymes involved in nitrogen fixation (nifH), nitrification (hao), denitrification (narG、nirK、norB、nosZ), and assimilatory and dissimilatory nitrogen reduction to ammonia (nasA、narB、napA、nirA、nirB、nrfA). Copy numbers of 16S rRNA genes of each detected phylotype of Danjiangkou Reservoir bacterioplankton were uniformly higher in water samples from Kuxin than in water samples from Qushou. Our analyses of differences in nitrogen abatement potential between water samples, based on bacterial community composition and function, provide a foundation for setting water environmental protection policies in the Danjiangkou Reservoir.

[Composition and Predictive Functional Analysis of Rhizosphere Bacterial Communities in Riparian Buffer Strips in the Danjiangkou Reservoir, China].

Microbial communities play crucial roles in the global biogeochemical nitrogen cycle. To our knowledge, the compositions and functions of rhizosphere communities in riparian buffer strips have not been reported. In this study, rhizosphere soil samples were collected from herbs (Vetiveria zizanioides and Phragmites australis), trees (Pyrus betulifolia), and shrubs (Discocleidion rufescens) in the Danjiangkou Reservoir in June 2017. High-throughput sequencing was performed to analyze the community structure and diversity of bacteria. Phylogenetic analysis based on 16S rDNA sequences shows that the bacterial communities can be divided into 31 major phylogenetic groups. The dominant phylogenetic groups include Proteobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, and Acidobacteria. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) was used to determine the metabolic and functional abilities of the observed bacterial communities. Our results reveal a wide genetic diversity of organisms involved in various essential processes such as biosynthesis of other secondary metabolites, transcription, Glycan biosynthesis and metabolism, cell growth and death, and carbohydrate metabolism. Based on the 16S rRNA gene copy number of the detected phylotype, the bacterial rhizospheres of plants in riparian buffer strips can be ranked as follows:Discocleidion rufescens > Phragmites australis > Vetiveria zizanioides > Pyrus betulifolia. We analyzed the differences of different plants from the perspective of bacterial community composition and function and provide a foundation for vegetation construction and water environmental protection in riparian buffer strips of the Danjiangkou Reservoir.