Massilia putida sp. nov., a dimethyl disulfide-producing bacterium isolated from wolfram mine tailing

Component specific responses of the microbiomes to common chemical stressors in the human food chain

Along a food chain, microbiomes occur in each component and often contribute to the functioning or the health of their host or environment. 'One Health' emphasizes the connectivity of each component's health. Chemical stress typically causes dysbiotic microbiomes, but it remains unclear whether chemical stressors consistently affect the microbiomes of food chain components. Here, we challenged food chain components, including water, sediments, soil, plants, and animals, with three chemical stresses consisting of arsenic (toxic trace element), benzoxazinoids (bioactive plant metabolites), and terbuthylazine (herbicide). We analysed 1064 microbiomes to assess their commonalities and differences in their stress responses. We found that chemical stressors overall decreased microbiome diversity in soil, but not in the other microbiomes. In response to stress, all food chain communities strongly shifted in their composition, generally becoming compositionally more similar to each other. In addition, we observed stochastic effects in host-associated communities (plant, animal). Dysbiotic microbiomes were characterized by different sets of bacteria, which responded specifically to the three chemical stressors. Microbial co-occurrence patterns significantly shifted with either decreased (water, sediment, plant, animal) or increased (soil) network sparsity and numbers of keystone taxa following stress treatments. These results suggest major re-distribution of specific taxa in the overall stress- and component-specific responses of microbiomes with the community stability of plant and animal microbiomes being the most affected by chemical stresses.

Description of Massilia orientalis sp. nov., Isolated from Rhizosphere Soil of Ageratina adenophora

A novel bacteria strain, designated YIM B02787T, was isolated from rhizosphere soil of Ageratina adenophora, in Yunnan, southwest China. The strain was aerobic, Gram-stain-negative, rod-shaped and motile with one polar flagellum. Growth occurred at 4-45 °C (optimum, 20-30 °C) and pH 6.0-10.0 (optimum, 7.0-8.0), and in presence of 0-1% (w/v) NaCl. Phylogenetic analyses based on both 16S rRNA gene and genome sequences data revealed that strain YIM B02787T belongs to the genus Massilia, being closely related to Massilia phosphatilytica KCTC 52513T (98.93% similarity), M. putida KCTC 42761T (98.86%), and M. kyonggiensis JCM 19189T (98.78%). The DNA G+C content was 65.9%. The digital DNA-DNA hybridization and average nucleotide identity values between the isolate strain and aforementioned closely neighbors were low, at 35.8-48.9 and 88.5-92.5%, respectively. Strain YIM B02787T contained Q-8 as the ubiquinone and major fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c, 45.5%) and C16:0 (27.5%). The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, two unidentified phospholipids, two unidentified aminophospholipids, and one unidentified polar lipid. On the basis of its phylogenetic, phenotypic and chemotaxonomic characteristics, strain YIM B02787Trepresents a novel species of the genus Massilia, for which the name Massilia orientalis sp. nov. is proposed. The type strain is YIM B02787T (= NBRC 116628T = CGMCC 1.61539T).

For aqueous/soil cadmium immobilization under acid attack, does the hydroxyapatite converted from Pseudochrobactrum sp. DL-1 induced vaterite necessarily show higher stability?

Microbial induced carbonate precipitation (MICP) technology was widely applied to immobilize heavy metals, but its long-term stability is tough to maintain, particularly under acid attack. This study successfully converted Pseudochrobactrum sp. DL-1 induced vaterite (a rare crystalline phase of CaCO3) to hydroxyapatite (HAP) at 30 ℃. The predominant conversion mechanism was the dissolution of CdCO3-containing vaterite and the simultaneous recrystallization of Ca4.03Cd0.97(PO4)3(OH)-containing HAP. For aqueous Cd immobilization, stability test at pH 2.0-10.0 showed that the Cd2+ desorption rate of Cd-adsorbed vaterite (3.96-4.35 ‱) were 7.13-20.84 times greater than that of Cd-adsorbed HAP (0.19-0.61 ‱). For soil Cd immobilization under 60 days of acid-rain erosion, the highest immobilization rate (51.00 %) of exchangeable-Cd and the lowest dissolution rate (-0.18 %) of carbonate-Cd were achieved with 2 % vaterite, while the corresponding rates were 16.78 % and 1.31 % with 2 % HAP, respectively. Furthermore, vaterite outperformed HAP in terms of soil ecological thorough evaluation. In conclusion, for Cd immobilization by MICP under acid attack, DL-1 induced vaterite displayed direct application value due to its exceptional stability in soil and water, while the mineral conversion strategy we presented is useful for further enhancing the stability in water.

Effects of mulch films with different thicknesses on the microbial community of tobacco rhizosphere soil in Yunnan laterite

The mulch film (MF) management model of the agricultural field affects the physical and chemical properties of soil (PCPS) and the structure of the microorganism community; however, studies on the relationship between the rhizosphere microorganism community structure and the thickness of MF are still limited. To understand the interactions among the MF thickness, PCPS, and rhizosphere microorganism, a study was conducted by using an integrated metagenomic strategy, where tobacco rhizosphere soil was treated with four commonly representative and used thicknesses of MFs (0.004, 0.006, 0.008, and 0.010 mm) in Yunnan laterite. The results showed that agronomic traits such as the tobacco plant height (TPH), leaf number (LN), fresh leaf weight (FLW), and dry leaf weight (DLW) were significantly (p < 0.01) improved in the field mulched with the thickest film (0.010 mm) compared with the exposed field (CK), and there was a 6.81 and 5.54% increase in the FLW and TPH, separately. The correlation analyses revealed a significant positive correlation of the MF thickness with the soil water content (SWC), soil organic matter (SOM), total nitrogen (TN), available nitrogen (AN), total phosphorus (TP), and available phosphorus (AP; all p < 0.01), while the MF thickness was negatively correlated with the soil temperature (ST; p < 0.01). In addition, the community structure of the rhizosphere soil bacteria was significantly changed overall by the MF thickness, which also interfered with the function of the rhizosphere soil bacteria. The correlation analyses also showed that the abundance of Bradyrhizobium and Nitrospira was positively correlated with the MF thickness, while the abundance of Sphinsinomonas and Massilia was negatively correlated with it. This indicated that with the increase of the MF thickness, the ability of the rhizosphere soil to utilize N and remove harmful molecules was strengthened, while the capacity of the rhizosphere soil to degrade pollutants was greatly reduced. These findings provide additional insights into the potential risks of the application of different thicknesses of MFs, particularly concerning the PCPS and soil microbial communities.

Response patterns of the microbiome during hexavalent chromium remediation by Tagetes erecta L

Chromium pollution, particularly hexavalent chromium [Cr(VI)], may threaten the environment and human health. This study investigated the potential of Tagetes erecta L. (Aztec marigold) for phytoremediation of soil contaminated with Cr(VI), and focused on the effects of varying concentrations of Cr(VI) on both the physicochemical properties of soil and microbiome of Tagetes erecta L. We observed that Tagetes erecta L. showed tolerance to Cr(VI) stress and maintained normal growth under these conditions, as indicated by bioconcentration factors of 0.33-0.53 in shoots and 0.39-0.70 in roots. Meanwhile, the structure and diversity of bacterial communities were significantly affected by Cr(VI) pollution. Specifically, Cr(VI) had a more significant effect on the microbial community structure in the endophytic of Tagetes erecta L. than in the rhizosphere (p < 0.05). The genera Devosia and Methylobacillus were positively correlated with Cr(VI) concentrations. Biomarkers such as Bacilli and Pseudonocardia were identified under the different Cr(VI)-contaminated treatments using LEfSe. In addition, the interaction and stability of the endophytic microbiome were enhanced under Cr(VI) stress. This study explored the interactions between heavy metals, microorganisms, and plants, providing valuable insights for developing in situ bioremediation of Cr(VI)-contaminated soils.

Differential effects of domesticated and wild Capsicum frutescens L. on microbial community assembly and metabolic functions in rhizosphere soil

Objective

Rhizosphere microorganisms play crucial roles in the growth and development of plants, disease resistance, and environmental adaptability. As the only wild pepper variety resource in China, domesticated Capsicum frutescens Linn. (Xiaomila) exhibits varying beneficial traits and affects rhizosphere microbial composition compared with its wild counterparts. In this study, we aimed to identify specific rhizosphere microbiome and metabolism patterns established during the domestication process.

Methods

The rhizosphere microbial diversity and composition of domesticated and wild C. frutescens were detected and analyzed by metagenomics. Non-targeted metabolomics were used to explore the differences of metabolites in rhizosphere soil between wild and domesticated C. frutescens.

Results

We found that the rhizosphere microbial diversity of domesticated variety was significantly different from that of the wild variety, with Massilia being its dominant bacteria. However, the abundance of certain beneficial microbes such as Gemmatimonas, Streptomyces, Rambibacter, and Lysobacter decreased significantly. The main metabolites identified in the wild variety included serylthreonine, deoxyloganic acid, vitamin C, among others. In contrast, those identified in the domesticated group were 4-hydroxy-l-glutamic acid and benzoic acid. Furthermore, the differentially enriched pathways were concentrated in tyrosine and tryptophan biosynthesis, histidine and purine-derived alkaloids biosynthesis, benzoic acid family, two-component system, etc.

Conclusion

This study revealed that C. frutescens established specific rhizosphere microbiota and metabolites during domestication, which has important significance for the efficient utilization of beneficial microorganisms in breeding and cultivation practices.

Massilia luteola sp. nov., a novel indole-producing and cellulose-degrading bacterium isolated from soil

A Gram-stain-negative, rod-shaped, indole-producing, and cellulose-degrading bacterial strain, designated NEAU-G-C5T, was isolated from soil collected from a forest in Dali city, Yunnan province, south China. 16S rRNA gene sequence analysis showed that strain NEAU-G-C5T was assigned to the genus Massilia and showed high sequence similarities to Massilia phosphatilytica 12-OD1T (98.32 %) and Massilia putida 6 NM-7T (98.41 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-G-C5T formed a lineage related to M. phosphatilytica 12-OD1T and M. putida 6 NM-7T. The major fatty acids of the strain were C16 : 0, C16 : 1 ω7c, and C17 : 0 cyclo. The respiratory quinone was Q-8. The polar lipid profile of the strain showed the presence of diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. In addition, the average nucleotide identity values between strain NEAU-G-C5T and its reference strains M. phosphatilytica 12-OD1T, M. putida 6 NM-7T, M. norwichensis NS9T, and M. kyonggiensis TSA1T were 89.7, 88.2, 81.3, and 88.0 %, respectively, and the levels of digital DNA-DNA hybridization between them were found to be 58.5 % (54.9-62.0 %), 53.2 % (49.8-56.7 %), 31.9 % (28.6-35.5 %), and 57.7 % (54.1-61.2 %), respectively, which were lower than the accepted threshold values of 95-96 % and 70 %, respectively. The DNA G+C content of strain NEAU-G-C5T was 66.5 mol%. The strain could produce indoleacetic acid and cellulase. On the basis of the phenotypic, genotypic, and chemotaxonomic characteristics, we conclude that strain NEAU-G-C5T represents a novel species of the genus Massilia, for which the name Massilia luteola sp. nov. is proposed. The type strain is NEAU-G-C5T (=MCCC 1K08668T=KCTC 8080T).

Diversity of Endophytes of Actinidia arguta in Different Seasons

The seasonal changes in environmental conditions can alter the growth states of host plants, thereby affecting the living environment of endophytes and forming different endophytic communities. This study employs Illumina MiSeq next-generation sequencing to analyze the 16SrRNA and ITS rDNA of endophytes in 24 samples of Actinidia arguta stem tissues across different seasons. The results revealed a high richness and diversity of endophytes in Actinidia arguta, with significant seasonal variations in microbial community richness. This study identified 897 genera across 36 phyla for bacteria and 251 genera across 8 phyla for fungi. Notably, 69 bacterial genera and 19 fungal genera significantly contributed to the differences in community structure across seasons. A distinctive feature of coexistence in the endophytic community, both specific and conservative across different seasons, was observed. The bacterial community in winter demonstrated significantly higher richness and diversity compared to the other seasons. Environmental factors likely influence the optimal timing for endophyte colonization. Solar radiation, temperature, precipitation, and relative humidity significantly impact the diversity of endophytic bacteria and fungi. In addition, seasonal variations show significant differences in the nutritional modes of fungal endophytes and the degradation, ligninolysis, and ureolysis functions of bacterial endophytes. This study elucidates the potential role of endophytes in assisting Actinidia arguta in adapting to seasonal changes and provides a theoretical basis for further exploration of functional microbial strains.

The impact of utilizing oyster shell soil conditioner on the growth of tomato plants and the composition of inter-root soil bacterial communities in an acidic soil environment

Introduction

The objective of this study is to examine the impact of various oyster shell soil conditioners, which are primarily composed of oyster shells, on the growth of tomatoes in acidic soil. Moreover, the aim of this investigation is to analyze the variety and structure of soil bacterial populations in close proximity to tomato roots while also contributing to the understanding of the physical, chemical, and biological mechanisms of oyster shell soil conditioners.

Methods

Tomato plants were grown in acidic red soil in three groups: a control group and a treatment group that used two types of oyster shell soil conditioners, OS (oyster shell powder) and OSF (oyster shell powder with organic microbial fertilizer). A range of soil physicochemical properties were measured to study differences in inter-soil physicochemical parameters and the growth of tomato plantings. In addition, this study utilized the CTAB (Cetyltrimethylammonium Bromide) technique to extract DNA from the soil in order to investigate the effects of oyster shell soil conditioner on the composition and diversity of bacterial populations. Utilizing high-throughput sequencing technologies and diversity index analysis, the composition and diversity of bacterial populations in the soil adjacent to plant roots were then evaluated. Ultimately, correlation analysis was used in this study to explore the relationship between environmental factors and the relative abundance of soil bacteria in the inter-root zone of tomato plants.

Results

The findings indicated that the oyster shell soil conditioners were capable of modifying the physicochemical characteristics of the soil. This was evidenced by significant increases in soil total nitrogen (16.2 and 59.9%), soil total carbon (25.8 and 27.7%), pH (56.9 and 55.8%), and electrical conductivity (377.5 and 311.7%) in the OS and OSF groups, respectively, compared to the control group (p < 0.05). Additionally, data pertaining to tomato seed germination and seedling growth biomass demonstrated that both oyster shell soil conditioners facilitated the germination of tomato seeds and the growth of seedlings in an acidic red clay soil (p < 0.05). On the other hand, the application of two oyster shell soil conditioners resulted in a modest reduction in the diversity of inter-root soil bacteria in tomato plants. Specifically, the group treated with OSF exhibited the most substantial fall in the diversity index, which was 13.6% lower compared to the control group. The investigation carried out on the soil between tomato plant roots yielded findings about the identification of the ten most abundant phyla. These phyla together represented 91.00-97.64% of the overall abundance. In the inter-root soil of tomatoes, a study identified four major phyla, namely Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, which collectively accounted for up to 85% of the total abundance. At the general level, the relative abundance of Massilia increased by 2.18 and 7.93%, Brevundimonas by 5.43 and 3.01%, and Lysobacter by 3.12 and 7.49% in the OS and OSF groups, respectively, compared to the control group. However, the pathogenic bacteria unidentified_Burkholderiaceae decreased by 5.76 and 5.05%, respectively. The correlation analysis yielded conclusive evidence indicating that, which involved the use of CCA (Canonical Correlation Analysis) graphs and Spearman correlation coefficients, pH exhibited a positive correlation (p < 0.05) with Shewanella and a negative correlation (p < 0.05) with Bradyrhizobium. The relative abundance of Lysobacter and Massilia exhibited a positive correlation with the levels of total soil nitrogen.

Discussion

The utilization of oyster shell soil conditioner on acidic red soil resulted in several positive effects. Firstly, it raised the pH level of the inter-root soil of tomato plants, which is typically acidic. This pH adjustment facilitated the germination of tomato seeds and promoted the growth of seedlings. In addition, the application of oyster shell soil conditioner resulted in changes in the structure of the bacterial community in the inter-root soil, leading to an increase in the relative abundance of Proteobacteria and Bacteroidetes and a decrease in the relative abundance of Acidobacteria. Furthermore, this treatment fostered the proliferation of genera of beneficial bacteria like Massilia, Brevundimonas, and Lysobacter, ultimately enhancing the fertility of the red soil.

Response behavior of antibiotic resistance genes and human pathogens to slope gradient and position: An environmental risk analysis in sloping cultivated land

Soils, especially in farmlands, are key media for the transmission of antibiotic resistance genes (ARGs) and their hosts from the environment to humans. Sloping farmland is an important agricultural resource, but there lack of studies on the fate and risk of ARGs in sloping land. Also, the behavior and drivers of ARGs in response to slope gradient and position are unclear. Here, metagenomics was used to investigate the profiles of ARGs, mobile genetic elements, and microbial communities in soils from lands of five slope gradients (5°, 10°, 15°, 20°, and 25°) with two slope positions (uphill and downhill). Results showed that while the abundance (except 15°) and diversity (except 20°) of ARGs increased as the slope gradient increased, the diversity of ARGs with health risk, especially the high-risk ones, decreased. For slope positions, abundant and diverse ARGs were more likely to accumulate at downhill. Furthermore, 52 bacterial genera and 12 human pathogenic bacteria (HPB) species were identified as the potential hosts for ARGs with high risk, and abundant HPB species were also detected in the soils with low gradients at downhill. Moreover, the structural equation model analysis revealed that the slope gradient and the slope position have both direct and indirect effects on the abundance of ARGs. Further correlation analysis revealed that the slope gradient has a positive effect (p < 0.05) on nitrite nitrogen in the soils. Also, the slope position has a negative effect (p < 0.05) on total phosphorus and microbial nitrogen, while positively affected (p < 0.05) on particulate nitrogen and microbial carbon, which were the key factors driving the behavior of ARGs. Overall, this study provided comprehensive information on ARGs with health risks and their potential pathogenic hosts in sloping farmland. It can be important for controlling antibiotic resistance transmission and be consistent with the One Health framework.

Bioplastic (poly-3-hydroxybutyrate)-producing Massilia endophytica sp. nov., isolated from Cannabis sativa L. 'Cheungsam'

A rod-shaped, motile, Gram-negative bacterial strain named DM-R-R2A-13T was isolated from the plant Cannabis sativa L. 'Cheungsam'. The phylogenetic analysis of the 16S rRNA gene sequence revealed that strain DM-R-R2A-13T belongs to the family Oxalobacteraceae and is closely related to members of the genus Massilia, with Massilia flava (97.58% sequence similarity) and Massilia armeniaca (97.37% sequence similarity) being the closest members. The digital DNA-DNA hybridization (dDDH) values between strain DM-R-R2A-13T and Massilia flava CGMCC 1.10685T and Massilia armeniaca ZMN-3Twere 22.2% and 23.3%, while the average nucleotide identity (ANI) values were 78.85% and 79.63%, respectively. The DNA G+C content was measured to be 64.6 mol%. Moreover, the bacterium was found to contain polyhydroxyalkanoate (PHA) granules based on transmission electron microscopy, indicating its potential to produce bioplastic. Genome annotation revealed the presence of PHA synthase genes (phaC, phaR, phaP, and phaZ), and the biopolymer was identified as poly-3-hydroxybutyrate (PHB) based on nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR) analyses. Using maltose as a carbon source, the strain produced PHB of up to 58.06% of its dry cell weight. Based on the phenotypic, chemotaxonomic, and phylogenetic characteristics, it has been determined that DM-R-R2A-13T represents a novel species belonging to the genus Massilia. As such, the name Massilia endophytica sp. nov. is proposed for this newly identified species. The type strain is DM-R-R2A-13T (= KCTC 92072T = GDMCC 1.2920T).

Using silkworm excrement to restore vegetation and soil ecology in heavily contaminated mining soils by multiple metal(loid)s: A recyclable sericulture measure

Ecological restoration of heavily contaminated soils by multiple metal(loid)s in mining areas is very difficult. In this study, we provided an attractive measure of using silkworm excrement (SE) and its modified materials to restore the soil heavily contaminated by arsenic (As), antimony (Sb), cadmium (Cd), lead (Pb) and chromium (Cr). We investigated the adsorption capacities and the associated remediation mechanisms for antimonite [Sb(III)] and antimonate [Sb(V)] by raw SE, biochar-modified SE (BC700), iron-modified BC700 (MBC) and sulfhydryl-modified BC700 (SH). Then, we selected SE and SH to compare their outcomes to restore the vegetations and the soil bacterial communities in the investigated soil mentioned above. The results showed that SE displayed the best characteristics for metal(loid) physical adsorption. But SH conferred the strongest capacity to adsorb Sb (max 23.92 mg g-1), suggesting the process of chemical adsorption played a key role in adsorbing Sb via functional groups (-SH). SE and SH both significantly (1) promoted the growth of pakchoi (Brassica campestris L., New Zealand No.2), community abundance of soil bacteria (283-936 OTUs), and the quantity of bacterial genera correlated with resistance, plant growth promotion and specified carbon metabolism; (2) but reduced bacterial genera correlated with pathogenicity. In this study, we suggested an attractive recyclable measure to restore the disturbed ecological environment in mining areas, i.e, using mulberry to restore the vegetation→ using leaves of mulberry to rear silkworms→ using SE to immobilize metal(loid)s in soils growing mulberry or other plants.

Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov

Based on genome-wide data, Massilia species belonging to the clade including Telluria mixta LMG 11547T should be entirely transferred to the genus Telluria owing to the nomenclatural priority of the type species Telluria mixta. This results in the transfer of 35 Massilia species to the genus Telluria. The presented data also supports the creation of two new genera since peripherally branching Massilia species are distinct from Telluria and other related genera. It is proposed that 13 Massilia species are transferred to Mokoshia gen. nov. with the type species designated Mokoshia eurypsychrophila comb. nov. The species Massilia arenosa is proposed to belong to the genus Zemynaea gen. nov. as the type species Zemynaea arenosa comb. nov. The genome-wide analysis was well supported by canonical ordination analysis of Enzyme Commission (EC) codes annotated from genomes via pannzer2. This new approach was performed to assess the conclusions of the genome-based data and reduce possible ambiguity in the taxonomic decision making. Cross-validation of EC code data compared within canonical plots validated the reclassifications and correctly visualized the expected genus-level taxonomic relationships. The approach is complementary to genome-wide methodology and could be used for testing sequence alignment based data across genetically related genera. In addition to the proposed broader reclassifications, invalidly described species 'Massilia antibiotica', 'Massilia aromaticivorans', 'Massilia cellulosiltytica' and 'Massilia humi' are described as Telluria antibiotica sp. nov., Telluria aromaticivorans sp. nov., Telluria cellulosilytica sp. nov. and Pseudoduganella humi sp. nov., respectively. In addition, Telluria chitinolytica is reclassified as Pseudoduganella chitinolytica comb. nov. The use of combined genome-wide and annotation descriptors compared using canonical ordination clarifies the taxonomy of Telluria and its sibling genera and provides another way to evaluate complex taxonomic data.

Dynamic distribution of Massilia spp. in sewage, substrate, plant rhizosphere/phyllosphere and air of constructed wetland ecosystem

Introduction

Massilia bacteria are widely distributed and have various ecological functions. Preliminary studies have shown that Massilia is the dominant species in constructed wetland ecosystems, but its species composition and distribution in constructed wetlands are still unclear.

Methods

In this paper, the in-house-designed primers were used to construct a 16S rDNA clone library of Massilia. The RFLP sequence analysis method was used to analyze the diversity of Massilia clone library and the composition of Massilia in sewage, substrate, plant rhizosphere, plant phyllosphere and air in a constructed wetland sewage treatment system. Redundancy analysis (RDA) and canonical correspondence analysis (CCA) were used to analyze the correlation between environmental factors and the population characteristics of Massilia in the corresponding environment. The dominant species of Massilia were analyzed for differences.

Results

The results showed that the 16S rDNA clone library in primer 5 worked well. According to the clone library diversity index analysis, the richness of Massilia varied significantly in different environments in different seasons, where the overall summer and autumn richness was higher than that in the spring and winter. The relative abundance of 5 Massilia in the constructed wetland ecosystem was greater than 1% in all samples, which were M. alkalitolerans, M. albidiflava, M. aurea, M. brevitalea, and M. timonae. The seasonal variation of dominant genera was significantly correlated with environmental factors in constructed wetlands.

Discussion

The above results indicated that the species of Massilia were abundant and widely distributed in the constructed wetland ecosystem, and there were significant seasonal differences. In addition, the Massilia clone library of constructed wetland was constructed for the first time in this study and the valuable data of Massilia community structure were provided, which was conducive to the further study of microbial community in constructed wetland.

Comparison of gut microbiota between immigrant and native populations of the Silver-eared Mesia (Leiothrix argentauris) living in mining area

The complex gut bacterial communities have a major impact on organismal health. However, knowledge of the effects of habitat change on the gut microbiota of wild birds is limited. In this study, we characterized the gut microbiota of two different subspecies of the Silver-eared Mesia (Leiothrix argentauris), the native subspecies (L. a. rubrogularis) and immigrant subspecies (L. a. vernayi), using 16S rRNA gene high-throughput sequencing. These two subspecies live in a trace metal-contaminated area, and L. a. vernayi was trafficked. They are an excellent system for studying how the gut microbiome of wild animal changes when they move to new habitats. We hypothesized that the immigrant subspecies would develop the same adaptations as the native subspecies in response to habitat changes. The results showed that there were no significant differences in the composition, diversity, or functional metabolism of gut microbiota between native and immigrant subspecies under the combined action of similar influencing factors (the p values of all analyses of variance >0.05). In addition, the composition and functional metabolism of gut microbiota in two subspecies showed adaptation against trace metal damage. Linear discriminant analysis effect size (LEfSe) analysis revealed that Massilia in the intestinal microbiota of immigrant subspecies was significantly higher than that of native subspecies, suggesting that immigrant subspecies suffered habitat change. Finally, we found that these two subspecies living in the mining area had an extremely high proportion of pathogenic bacteria in their gut microbiota (about 90%), much higher than in other species (about 50%) living in wild environment. Our results revealed the adaptation of intestinal microbiota of immigrant Silver-eared Mesias under heavy metals stress, which would provide guidance for biodiversity conservation and pollution management in mining area.

Massilia phyllostachyos sp. nov., Isolated from the Roots of Moso Bamboo in China

A Gram-negative, strictly aerobic, motile, and rod-shaped bacterial strain G4R7^T was isolated from the roots of moso bamboo (Phyllostachys edulis) in Zhejiang, Hangzhou Province, China. After comparing 16S rRNA gene sequences, strain G4R7^T exhibited the highest similarities with Massilia neuiana PTW21^T (98.3%), followed by M. agri K-3-1^T (98.3%), M. consociate CCUG 58010^T (97.7%), M. niastensis 5516S-1^T (97.7%) and M. yuzhufengensis ZD1-4^T (97.6%). The phylogenetic analysis revealed that strain G4R7^T belonged to the genus Massilia. The draft genome of strain G4R7^T was 5.81 Mb, and the G+C content was 64.4%. The average nucleotide identity values between G4R7^T and another related member of the genus Massilia ranged from 76.6 to 87.2%, and the digital DNA-DNA hybridization ranged from 20.7 to 27.9%. Strain G4R7^T grew at 15-37 °C (optimum 25-30 °C) and pH 6.0-9.0 (optimum pH 7.0) in the presence of 0-3% (w/v) NaCl (optimum 0%). The respiratory quinone was Q-8, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and aminophospholipid. The major cellular fatty acids were C_10:0 3OH, C_12:0, C_12:0 2OH, and C_16:0, summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c). As per the data from chemotaxonomic, phylogenetic, and phenotypic evidence, strain G4R7^T represents a new species of genus Massilia, for which the name Massilia phyllostachyos sp. nov. is proposed. The type strain is G4R7^T (=ACCC 61911^T=GDMCC 1.2961^T=JCM 35225^T).

Unique or not unique? Comparative genetic analysis of bacterial O-antigens from the Oxalobacteraceae family

Many plants and animals have symbiotic relationships with microorganisms, including bacteria. The interactions between bacteria and their hosts result in different outcomes for the host organism. The outcome can be neutral, harmful or have beneficial effects for participants. Remarkably, these relationships are not static, as they change throughout an organism's lifetime and on an evolutionary scale. One of the structures responsible for relationships in bacteria is O-antigen. Depending on the characteristics of its components, the bacteria can avoid the host's immune response or establish a mutualistic relationship with it. O-antigen is a key component in Gram-negative bacteria's outer membrane. This component facilitates interaction between the bacteria and host immune system or phages. The variability of the physical structure is caused by the genomic variability of genes encoding O-antigen synthesis components. The genes and pathways of O-polysaccharide (OPS) synthesis were intensively investigated mostly for Enterobacteriaceae species. Considering high genetic and molecular diversity of this structure even between strains, these findings may not have caught the entire variety possibly presented in non-model species. The current study presents a comparative analysis of genes associated with O-antigen synthesis in bacteria of the Oxalobacteraceae family. In contrast to existing studies based on PCR methods, we use a bioinformatics approach and compare O- antigens at the level of clusters rather than individual genes. We found that the O-antigen genes of these bacteria are represented by several clusters located at a distance from each other. The greatest similarity of the clusters is observed within individual bacterial genera, which is explained by the high variability of O-antigens. The study describes similarities of OPS genes inherent to the family as a whole and also considers individual unique cases of O-antigen genetic variability inherent to individual bacteria.

Duganella dendranthematis sp. nov. and Massilia forsythiae sp. nov., isolated from flowers

Two aerobic, Gram-stain-negative, motile, mesophilic, rod-shaped and catalase-positive bacterial strains designated AF9R3T and GN2-R2T were isolated from flowers collected in the Republic of Korea. Strain AF9R3T grew at 4–33 °C, pH 4.0–9.0 and with 0–1 % NaCl (w/v), and strain GN2-R2T grew at 10–33 °C, pH 4.0–9.0 and with 0–1 % NaCl (w/v). Phylogenetic analysis on the basis of 16S rRNA gene sequences indicated that strains AF9R3T and GN2-R2T belonged to the genera Duganella and Massilia , respectively, showing high sequence similarity to Duganella levis CY42WT (99.4 %) and Massilia putida 6 NM-7T (98.0 %), respectively. Both strains contained summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and C16 : 0 as the major fatty acids, and ubiquinone Q-8 as the predominant quinone. Strain AF9R3T had diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and strain GN2-R2T comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the major polar lipids. Orthologous average nucleotide identity and digital DNA–DNA hybridization values of strain AF9R3T to its closest relative D. levis CY42WT were 92.6 and 56.5 %, and those of strain GN2-R2T to its closest relative M. putida 6 NM-7T were 81.4 and 24.8 %. Based on genotypic and phenotypic data, strains AF9R3T and GN2-R2T are considered to represent novel species of the genus Duganella and Massilia , respectively, for which the names Duganella dendranthematis sp. nov. (type strain AF9R3T=KACC 21258T=NBRC 114510T) and Massilia forsythiae sp. nov. (type strain GN2-R2T=KACC 21261T=NBRC 114511T) have been proposed.

The role of microplastics in altering arsenic fractionation and microbial community structures in arsenic-contaminated riverine sediments

The ability of microplastics (MPs) to interact with environmental pollutants is of great concern. Riverine sediments, as sinks for multi-pollutants, have been rarely studied for MPs risk evaluation. Meanwhile, MPs generated from biodegradable plastics are questioning the safety of the promising materials. In this study, we investigated the effects of typical non-degradable polyethylene (PE) and biodegradable polylactic acid (PLA) MPs on sediment enzymes, arsenic (As) fractionation, and microbial community structures in As-contaminated riverine sediments. The results indicated that the presence of MPs (1% and 3%, w/w) led As transformed into more labile and bioavailable fractions in riverine sediments, especially under higher As and MPs levels. Analysis on microbial activities and community structures confirmed the strong potential of MPs in inhibiting microbial activities and shifting bacterial community succession patterns through enrichment of certain microbiota. Moreover, biodegradable PLA MPs presented stronger alterations in arsenic fractionation and microbial community structures than PE MPs did, which might be jointly attributed to adsorption behaviors, microbial alterations, and potential PLA degradation behaviors. The study indicated that MPs contamination increased As mobility and bioavailability, and shifted microbial communities in riverine sediments. Moreover, biodegradable MPs might lead to stronger microbial alterations and increases in As bioavailability, acting as a threat to ecological safety, which needed further exploration.

Characterisation of Waterborne Psychrophilic Massilia Isolates with Violacein Production and Description of Massilia antarctica sp. nov

A group of seven bacterial strains producing blue-purple pigmented colonies on R2A agar was isolated from freshwater samples collected in a deglaciated part of James Ross Island and Eagle Island, Antarctica, from 2017–2019. The isolates were psychrophilic, oligotrophic, resistant to chloramphenicol, and exhibited strong hydrolytic activities. To clarify the taxonomic position of these isolates, a polyphasic taxonomic approach was applied based on sequencing of the 16S rRNA, gyrB and lepA genes, whole-genome sequencing, rep-PCR, MALDI-TOF MS, chemotaxonomy analyses and biotyping. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the entire group are representatives of the genus Massilia. The closest relatives of the reference strain P8398T were Massilia atriviolacea, Massilia violaceinigra, Massilia rubra, Massilia mucilaginosa, Massilia aquatica, Massilia frigida, Massilia glaciei and Massilia eurypsychrophila with a pairwise similarity of 98.6–100% in the 16S rRNA. The subsequent gyrB and lepA sequencing results showed the novelty of the analysed group, and the average nucleotide identity and digital DNA–DNA hybridisation values clearly proved that P8398T represents a distinct Massilia species. After all these results, we nominate a new species with the proposed name Massilia antarctica sp. nov. The type strain is P8398T (= CCM 8941T = LMG 32108T).

Ecological floating bed for decontamination of eutrophic water bodies: Using alum sludge ceramsite

In this study, a combined ecological floating bed (C-EFB) with alum sludge ceramsite (ASC) was designed to improve the water purification effect of traditional ecological floating beds (T-EFBs). During the ASC preparation stage, alum sludge was shaped into a ball, air-dried, and fired under 600 °C. The physical and chemical properties of the ASC meet the requirements of Artificial Ceramsite Filter Materials for Water Treatment (CJ/T229-2008). This study investigated the increased capability of this new-type artificial substrate (ASC) on the removal of chemical oxygen demand (COD), ammonia nitrogen (NH4+-N), total phosphorus (TP), and total nitrogen (TN) from eutrophic landscape water. Compared with the T-EFB, the C-EFB owns a higher purification efficiency. The highest average efficiency of COD, NH4+-N, TN and TP removals during the four operating stages was 78.2%, 58.1%, 46.7% and 53.2%, respectively, in the C-EFB, which were all higher than those of 53.5%, 32.4%, 27.2% and 25.8%, respectively, for the T-EFB. Among them, the C-EFB showed a higher advantage in the removal of TP. The results showed that the potential benefits of utilizing ASC in seriously eutrophic bodies of water.

Massilia rhizosphaerae sp. nov., a rice-associated rhizobacterium with antibacterial activity against Ralstonia solanacearum

A novel rhizobacterium, designated strain NEAU-GH312^T, with antibacterial activity against Ralstonia solanacearum was isolated from rhizosphere soil of rice (Heilongjiang Province, PR China) and characterized with a polyphasic approach. Cells of strain NEAU-GH312^T were Gram-stain-negative, aerobic, non-spore-forming, motile with peritrichous flagella and rod-shaped. Colonies were light orange, convex and semi-translucent on Reasoner's 2A (R2A) agar after 2 days of incubation at 28 °C. Growth was observed on R2A agar at 10-40 °C, pH 4.0-8.0 and with 0-5 % (w/v) NaCl. The respiratory quinone was ubiquinone Q-8. The major cellular fatty acids of strain NEAU-GH312^T were C_16 : 1  ω7c and/or C_16 : 1  ω6c, C_16 : 0 and C_18 : 1  ω7c and/or C_18 : 1  ω6c. The main polar lipids were phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Phylogenetic analyses confirmed the well-supported affiliation of strain NEAU-GH312^T within the genus Massilia, close to the type strains of Massilia arvi THG-RS2O^T (98.7 %), Massilia norwichensis NS9^T (98.7 %) and Massilia kyonggiensis TSA1^T (98.6 %). Strain NEAU-GH312^T had a genome size of 6.68 Mb and an average DNA G+C content of 66.3 mol%. Based on the genotypic, phenotypic and chemotaxonomic data obtained in this study, strain NEAU-GH312^T could be classified as representative of a novel species of the genus Massilia, for which the name Massilia rhizosphaerae sp. nov. is proposed, with strain NEAU-GH312^T (=DSM 109722^T=CCTCC AB 2019142^T) as the type strain.

Draft Genome Sequences of the Three Massilia Strains AB1, ST3, and ZL223

To increase the genomic data available for antibiotic discovery, three independently isolated antibiotic-producing Massilia strains were sequenced. No more than 84% average nucleotide identity was shared with publicly available Massilia genomes, and a low similarity of predicted biosynthetic gene clusters to known clusters was found.

Massilia cellulosiltytica sp. nov., a novel cellulose-degrading bacterium isolated from rhizosphere soil of rice (Oryza sativa L.) and its whole genome analysis

A bacterial strain, Gram-stain negative, rod-shaped, aerobic and cellulose-degrading, designated NEAU-DD11^T, was isolated from rhizosphere soil of rice collected from Northeast Agricultural University in Harbin, Heilongjiang Province, North-east China. Base on 16S rRNA gene sequence analysis, strain NEAU-DD11^T belongs to the genus Massilia and shared high sequence similarities with Massilia phosphatilytica 12-OD1^T (98.46%) and Massilia putida 6NM-7 ^T (98.41%). Phylogenetic analysis based on the 16S rRNA gene and whole genome sequences indicated that strain NEAU-DD11^T formed lineage related to M. phosphatilytica 12-OD1^T and M. putida 6NM-7 ^T. The major fatty acids of the strain were C_16:0, C_17:0-cyclo and C_16:1ω7c. The respiratory quinone was Q-8. The polar lipids profile of the strain showed the presence of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified polar lipid and an unidentified phospholipid. In addition, the digital DNA-DNA hybridization values between strain NEAU-DD11^T and M. phosphatilytica 12-OD1^T and M. putida 6NM-7 ^T were 45.4 and 35.6%, respectively, which are lower than the accepted threshold value of 70%. The DNA G + C content of strain NEAU-DD11^T was 66.2%. The whole genome analysis showed the strain contained carbohydrate enzymes such as glycoside hydrolase and polysaccharide lyase, which enabled the strain to have the function of degrading cellulose. On the basis of the phenotypic, genotypic and chemotaxonomic characteristics, we conclude that strain NEAU-DD11^T represents a novel species of the genus Massilia, for which the name Massilia cellulosiltytica sp. nov. is proposed. The type strain is NEAU-DD11^T (= CCTCC AB 2019141 ^T = DSM 109721 ^T).

Comparative Transcriptome and Endophytic Bacterial Community Analysis of Morchella conica SH

The precious rare edible fungus Morchella conica is popular worldwide for its rich nutrition, savory flavor, and varieties of bioactive components. Due to its high commercial, nutritional, and medicinal value, it has always been a hot spot. However, the molecular mechanism and endophytic bacterial communities in M. conica were poorly understood. In this study, we sequenced, assembled, and analyzed the genome of M. conica SH. Transcriptome analysis reveals significant differences between the mycelia and fruiting body. As shown in this study, 1,329 and 2,796 genes were specifically expressed in the mycelia and fruiting body, respectively. The Gene Ontology (GO) enrichment showed that RNA polymerase II transcription activity-related genes were enriched in the mycelium-specific gene cluster, and nucleotide binding-related genes were enriched in the fruiting body-specific gene cluster. Further analysis of differentially expressed genes in different development stages resulted in finding two groups with distinct expression patterns. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment displays that glycan degradation and ABC transporters were enriched in the group 1 with low expressed level in the mycelia, while taurine and hypotaurine metabolismand tyrosine metabolism-related genes were significantly enriched in the group 2 with high expressed level in mycelia. Moreover, a dynamic shift of bacterial communities in the developing fruiting body was detected by 16S rRNA sequencing, and co-expression analysis suggested that bacterial communities might play an important role in regulating gene expression. Taken together, our study provided a better understanding of the molecular biology of M. conica SH and direction for future research on artificial cultivation.

Study on the regulatory mechanism of the earthworm microbial community in vitro and in vivo under cadmium stress

In this paper, cadmium (Cd) stress tests were performed on Eisenia fetida in sterile artificial soil, and its regulatory mechanism between microbial communities in vivo and in vitro after Cd stress was explored. In the test, 0, 50, 100, 125, 250 and 500 mg kg^-1 Cd stress concentrations were implemented. After long-term and short-term stress, the microbes in the earthworms and the soil were cultured with ECO plates. The data statistics of carbon source utilization intensity were carried out using the method developed by our team. CCA was scientifically integrated into TOPSIS to establish a new data analysis model to find the regulatory nodes after stress (Ning et al., 2020). Macro gene sequencing technology revealed that the species with the highest absolute abundance in the microbial communities in vivo and in vitro were all unnamed new species. It was confirmed that the HBA gene, NEUROD1 gene and ABCA3 gene were the regulatory genes of the microbial community in the earthworms under Cd stress, while the TC.FEV.OM gene and cheBR gene were the main regulatory genes of the microbial community in the soil. These results provide a scientific and theoretical reference and model basis for the bioremediation of Cd-contaminated soil and the detoxification mechanism of earthworms.

Cold-shock gene cspC in the genome of Massilia polaris sp. nov. revealed cold-adaptation

A straw coloured, motile and Gram-stain-negative bacterium, designated RP-1-19^T was isolated from soil of Arctic station, Svalbard, Norway. Based on the phylogenetic analysis of its 16S rRNA gene sequence, strain RP-1-19^T formed a lineage within the family Oxalobacteraceae and clustered together within the genus Massilia. The closest members were M. violaceinigra B2^T (98.6% sequence similarity), M. eurypsychrophilia JCM 30074^T (98.3%) and M. atriviolacea SOD^T (98.1%). The only respiratory quinone was ubiquinone-8. The principal cellular fatty acids were summed feature 3 (iso-C_15:0 2-OH/C_16:1ω7c) and C_16:0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G + C content of the type strain was 63.2%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain RP-1-19^T and closest members were ≤ 80 and 23.2%, respectively. The genome was 4,522,469 bp long with 30 scaffolds and 4076 protein-coding genes. The genome showed eight putative biosynthetic gene clusters responsible for various secondary metabolites. Genome analysis revealed the presence of cold-shock proteins CspA and CspC. Presence of cspA and cspC genes in the genome manifest ecophysiology of strain RP-1-19^T that may help in cold-adaptation. Based on these data, strain RP-1-19^T represents a novel species in the genus Massilia, for which the name Massilia polaris sp. nov. is proposed. The type strain is RP-1-19^T (= KACC 21619^T = NBRC 114359^T).

Massilia horti sp. nov. and Noviherbaspirillum arenae sp. nov., two novel soil bacteria of the Oxalobacteraceae

We isolated two new soil bacteria: ONC3^T (from garden soil in NC, USA; LMG 31738^T=NRRL B-65553^T) and M1^T (from farmed soil in MI, USA; NRRL B-65551^T=ATCC TSD-197^T=LMG 31739^T) and characterized their metabolic phenotype based on Biolog, MALDI-TOF MS and fatty acid analyses, and compared 16S rRNA and whole genome sequences to other members of the Oxalobacteraceae after sequencing on an Illumina Nextera platform. Based on the results of 16S rRNA sequence analysis, ONC3^T shows the highest sequence similarity to Massilia solisilvae J18^T (97.8 %), Massilia terrae J11^T (97.7 %) and Massilia agilis J9^T (97.3 %). Strain M1^T is most closely related to Noviherbaspirillum denitrificans TSA40^T, Noviherbaspirillum agri K-1-15^T and Noviherbaspirillum autotrophicum TSA66^T (sequence identity of 98.2, 98.0 and 97.8 %, respectively). The whole genome of ONC3^T has an assembled size of 5.62 Mbp, a G+C content of 63.8 mol% and contains 5104 protein-coding sequences, 56 tRNA genes and two rRNA operons. The genome of M1^T has a length of 4.71 MBp, a G+C content of 63.81 mol% and includes 4967 protein-coding genes, two rRNA operons and 44 tRNA genes. Whole genome comparisons identified Massilia sp. WG5 with a 79.3 % average nucleotide identity (ANI) and 22.6 % digital DNA-DNA hybridization (dDDH), and Massilia sp. UBA11196 with 78.2 % average amino acid identity (AAI) as the most closely related species to ONC3^T. M1^T is most closely related to N. autotrophicum TSA66^T with an ANI of 80.27 %, or N. denitrificans TSA40^T with a dDDH of 22.3 %. The application of community-accepted standards such as <98.7 % in 16S sequence similarity and <95-96 % ANI or 70 % DDH support the classification of Massilia horti ONC3^T and Noviherbaspirillum arenae M1^T as novel species within the Oxalobacteraceae.

Genome insight and description of antibiotic producing Massilia antibiotica sp. nov., isolated from oil-contaminated soil

An ivory-coloured, motile, Gram-stain-negative bacterium, designated TW-1^T was isolated from oil-contaminated experimental soil in Kyonggi University. The phylogenetic analysis based on 16S rRNA gene sequence revealed, strain TW-1^T formed a lineage within the family Oxalobacteraceae and clustered as members of the genus Massilia. The closest members were M. pinisoli T33^T (98.8% sequence similarity), M. putida 6NM-7^T (98.6%), M. arvi THG-RS2O^T (98.5%), M. phosphatilytica 12-OD1^T (98.3%) and M. niastensis 5516S-1^T (98.2%). The sole respiratory quinone is ubiquinone-8. The major cellular fatty acids are hexadeconic acid, cis-9, methylenehexadeconic acid, summed feature 3 and summed feature 8. The major polar lipids are phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G + C content of the type strain is 66.3%. The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain TW-1^T and closest members were below the threshold value for species demarcation. The genome size is 7,051,197 bp along with 46 contigs and 5,977 protein-coding genes. The genome showed 5 putative biosynthetic gene clusters (BGCs) that are responsible for different secondary metabolites. Cluster 2 showed thiopeptide BGC with no known cluster blast, indicating TW-1^T might produce novel antimicrobial agent. The antimicrobial assessment also showed that strain TW-1^T possessed inhibitory activity against Gram-negative pathogens (Escherichia coli and Pseudomonas aeruginosa). This is the first report of the species in the genus Massilia which produces antimicrobial compounds. Based on the polyphasic study, strain TW-1^T represents novel species in the genus Massilia, for which the name Massilia antibiotica sp. nov. is proposed. The type strain is TW-1^T (= KACC 21627^T = NBRC 114363^T).

Analysis of microbial diversity and functional differences in different types of high-temperature Daqu

Bacterial communities that enrich in high-temperature Daqu are important for the Chinese maotai-flavor liquor brewing process. However, the bacterial communities in three different types of high-temperature Daqu (white Daqu, black Daqu, and yellow Daqu) are still undercharacterized. In this study, the bacterial diversity of three different types of high-temperature Daqu was investigated using Illumina MiSeq high-throughput sequencing. The bacterial community of high-temperature Daqu is mainly composed of thermophilic bacteria, and seven bacterial phyla along with 262 bacterial genera were identified in all 30 high-temperature Daqu samples. Firmicutes, Actinobacteria, Proteobacteria, and Acidobacteria were the dominant bacterial phyla in high-temperature Daqu samples, while Thermoactinomyces, Staphylococcus, Lentibacillus, Bacillus, Kroppenstedtia, Saccharopolyspora, Streptomyces, and Brevibacterium were the dominant bacterial genera. The bacterial community structure of three different types of high-temperature Daqu was significantly different (p < .05). In addition, the results of microbiome phenotype prediction by BugBase and bacterial functional potential prediction using PICRUSt show that bacteria from different types of high-temperature Daqu have similar functions as well as phenotypes, and bacteria in high-temperature Daqu have vigorous metabolism in the transport and decomposition of amino acids and carbohydrates. These results offer a reference for the comprehensive understanding of bacterial diversity of high-temperature Daqu.

Massiliamide, a cyclic tetrapeptide with potent tyrosinase inhibitory properties from the Gram-negative bacterium Massilia albidiflava DSM 17472T

A cyclic tetrapeptide, designated massiliamide, was isolated from the liquid culture of the Gram-negative bacterium Massilia albidiflava DSM 17472^T. The structure was elucidated through extensive spectroscopic analysis, including HR-MS and 1D and 2D NMR experiments. The absolute configuration was determined using the Marfey´s method. Massiliamide showed potent inhibitory activity towards tyrosinase with an IC₅₀ value of 1.15 µM and no cytotoxicity.

How does the microenvironment change during the stabilization of cadmium in exogenous remediation sediment?

The pollution degree of heavy metals is closely related to the sediment microenvironment. This study aims to give a comprehensive account of the changes of microenvironment in sediment during the stabilization of cadmium (Cd) by the sodium lignosulphonate (SLS) modified chlorapatites (SLS@nClAP). Chemical speciation change demonstrated that SLS@nClAP possessed better stabilizing capacity (65.84 %-76.66 %) for Cd than unmodified chlorapatites (ClAP) (45.88 %). It might be since that the surface of SLS@nClAP presented a more dispersive thin sheet structure with sulfonate groups compared with the aggregate block structure of ClAP. High-throughput sequencing results displayed that succession of microbial community occurred after remediation in sediment. Most importantly, the dominant genus changed from massilia to phosphate-solubilizing bacterium-pseudomonas which might be due to the remediation of chlorapatites and the stabilization of Cd. Moreover, enzyme activity changes showed that the activity of catalase and urease were highly influenced by the stability and bioavailability of Cd during the incubation. This study not only provided a novel remediation technology for Cd-polluted sediment but also confirmed that the change of microenvironment was closely related to the stability and bioavailability of Cd in sediment.

Changes of root microbial populations of natively grown plants during natural attenuation of V-Ti magnetite tailings

Mine tailings contain dangerously high levels of toxic metals which pose a constant threat to local ecosystems. Few naturally grown native plants can colonize tailings site and the existence of their root-associated microbial populations is poorly understood. The objective of this study was to give further insights into the interactions between native plants and their microbiota during natural attenuation of abandoned V-Ti magnetite mine tailings. In the present work, we first examined the native plants' potential for phytoremediation using plant/soil analytical methods and then investigated the root microbial communities and their inferred functions using 16 S rRNA-based metagenomics. It was found that in V-Ti magnetite mine tailings the two dominant plants Bothriochloa ischaemum and Typha angustifolia were able to increase available nitrogen in the rhizosphere soil by 23.3% and 53.7% respectively. The translocation factors (TF) for both plants indicated that B. ischaemum was able to accumulate Pb (TF = 1.212), while T. angustifolia was an accumulator of Mn (TF = 2.502). The microbial community structure was more complex in the soil associated with T. angustifolia than with B. ischaemum. The presence of both plants significantly reduced the population of Acinetobacter. Specifically, B. ischaemum enriched Massilia, Opitutus and Hydrogenophaga species while T. angustifolia significantly increased rhizobia species. Multivariate analyses revealed that among all tested soil variables Fe and total organic carbon (TOC) could be the key factors in shaping the microbial structure. The putative functional analysis indicated that soil sample of B. ischaemum was abundant with nitrate/nitrite reduction-related functions while that of T. angustifolia was rich in nitrogen fixing functions. The results indicate that these native plants host a diverse range of soil microbes, whose community structure can be shaped by plant types and soil variables. It is also possible that these plants can be used to improve soil nitrogen content and serve as bioaccumulators for Pb or Mn for phytoremediation purposes.

Description of Massilia rubra sp. nov., Massilia aquatica sp. nov., Massilia mucilaginosa sp. nov., Massilia frigida sp. nov., and one Massilia genomospecies isolated from Antarctic streams, lakes and regoliths

Bacteria of the genus Massilia often colonize extreme ecosystems, however, a detailed study of the massilias from the Antarctic environment has not yet been performed. Here, sixty-four Gram-stain-negative, aerobic, motile rods isolated from different environmental samples on James Ross Island (Antarctica) were subjected to a polyphasic taxonomic study. The psychrophilic isolates exhibited slowly growing, moderately slimy colonies revealing bold pink-red pigmentation on R2A agar. The set of strains exhibited the highest 16S rRNA gene sequence similarities (99.5-99.9%) to Massilia violaceinigra B2^T and Massilia atriviolacea SOD^T and formed several phylogenetic groups based on the analysis of gyrB and lepA genes. Phenotypic characteristics allowed four of them to be distinguished from each other and from their closest relatives. Compared to the nearest phylogenetic neighbours the set of six genome-sequenced representatives exhibited considerable phylogenetic distance at the whole-genome level. Bioinformatic analysis of the genomic sequences revealed a high number of putative genes involved in oxidative stress response, heavy-metal resistance, bacteriocin production, the presence of putative genes involved in nitrogen metabolism and auxin biosynthesis. The identification of putative genes encoding aromatic dioxygenases suggests the biotechnology potential of the strains. Based on these results four novel species and one genomospecies of the genus Massilia are described and named Massilia rubra sp. nov. (P3094^T=CCM 8692^T=LMG 31213^T), Massilia aquatica sp. nov. (P3165^T=CCM 8693^T=LMG 31211^T), Massilia mucilaginosa sp. nov. (P5902^T=CCM 8733^T=LMG 31210^T), and Massilia frigida sp. nov. (P5534^T=CCM 8695^T=LMG 31212^T).

Massilia arenae sp. nov., isolated from sand soil in the Qinghai–Tibetan Plateau

A bacterial strain, designated GEM5T, was isolated from sand soil samples from the Qinghai–Tibet Plateau. The polyphasic study confirmed the affiliation of the isolate with the genus Massilia . GEM5T had Gram-stain-negative, non-spore-forming and rod-shaped cells and grew at 4–30 °C, pH 6–8 and with 0–2 % (w/v) NaCl. Its cell wall contained ribose. Q8 was the predominant respiratory quinone, and summed feature 3 (C16 : 1ω6c/ω7c) and C16 : 0 were the major components of the fatty acids. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and four unidentified lipids. The DNA G+C content was 65.1 mol%. The phylogenetic analysis based on the 16S rRNA gene showed a stable clade being formed by GEM5T, Massilia timonae CCUG 45783T (97.94 %) and Massilia oculi CCUG 43427AT (97.58 %). The average nucleotide identity (ANIb) values between GEM5T and M. timonae CCUG 45783T, M.oculi CCUG 43427AT were 91.3 and 91.7 %, respectively. On the basis of the morphological, physiological and chemotaxonomic pattern, it was proposed that strain GEM5T (=JCM 32744T=CICC 24458T) should be classified as representing a member of the genus Massilia with the name Massilia arenae sp. nov.

Methylobacterium nonmethylotrophicum sp. nov., isolated from tungsten mine tailing

A novel pink-pigmented strain, designated 6HR-1^T, was isolated from tungsten mine tailings in Jiangxi Province, PR China. Cells were Gram-stain-negative, aerobic, non-spore-forming, rod-shaped and motile with a polar flagellum (monotrichous). It could not utilize methanol, methylamine, formaldehyde or formate as a sole carbon source. The methanol dehydrogenase mxaF gene was absent but the xoxF gene was present. Phylogenomic and 16S rRNA gene phylogenetic analyses clearly showed that strain 6HR-1^T was affiliated to the genus Methylobacterium and closely related to 'Methylobacterium terrae' 17Sr1-28^T (98.6 %), Methylobacterium platani JCM 14648^T (97.7 %), Methylobacterium variabile DSM 16961^T (97.7 %) and Methylobacterium currus KACC 19662^T (97.4 %). The average nucleotide identity and digital DNA-DNA hybridization values between strain 6HR-1^T and its closely related type species were 87.4-88.7 and 33.2-36.3 %, respectively. It had summed feature 8 (C_{18 : 1} ω7c and/or C_{18 : 1} ω6c) as the major fatty acid and ubiquinone 10 as the predominant respiratory quinone. Polyphasic characterization supported that strain 6HR-1^T represents a novel species of the genus Methylobacterium, for which the name Methylobacterium nonmethylotrophicum sp. nov. is proposed with the type strain 6HR-1^T (=GDMCC 1.662^T=KCTC 42760^T).

Effect of tungsten-resistant bacteria on uptake of tungsten by lettuce and tungsten speciation in plants

Tungsten is an emerging contaminant because of its potential toxicity to humans. However, tungsten-plant-microbe interactions remains unknown. The objective of the study was to evaluate the effect of tungsten-resistant bacteria on tungsten species in plants and microbial community structure in soil. Although bacterial inoculation did not affect lettuce (Lactuca sativa L.) growth or tungsten uptake via root, tungsten-resistant bacteria increased translocation of tungsten from root to shoot. Bacterial inoculation slightly oxidized tungsten in lettuce based on tungsten L3 x-ray absorption near-edge structure (XANES). Tungsten in lettuce roots and shoots grown in tungsten(VI)-spiked soil existed as a mixture of tungsten(IV) and tungsten(VI). Tungsten accumulated as polytungstate in the root and monotungstate in the shoot. Inoculation with tungsten-resistant bacteria and plant growth increased microbial diversity in tungsten-contaminated soil. In tungsten-spiked soils without plants, metal-resistant or reducing bacteria were found while bacteria growing in rhizosphere were detected in soils supporting plant growth. These results indicate a role of the bacteria and plants in phytoremediation of tungsten-contaminated soil.

Significant Impacts of Both Total Amount and Availability of Heavy Metals on the Functions and Assembly of Soil Microbial Communities in Different Land Use Patterns

Land use change alters the accumulation of heavy metals (HMs) in soils and might have significant influence on the assembly and functions of soil microbial community. Although numerous studies have discussed the impacts of either total amounts or availability of metals on soil microbes in land change, there is still limited understanding on which one is more critical. In the present study, soils from three land use types (forest, mining field, and operating factory) located in Shaoguan city (Guangdong Province, China) were collected to investigate the impacts of soil HMs on soil enzyme activities and bacterial community structures. Mining activities remarkably increased the concentrations of HMs in soils, and land use patterns changed soil properties and nutrition level. Soil pH, total and available HMs (Cu, Pb, Zn, and Cd) and organic matters (SOM) were identified as the key influential factors shaping soil ecological functions (soil enzyme activities) and community assembly (bacterial community composition), explained by HMs accumulation and soil acidification caused by human activities. In addition, total amount and availability of some metals (Zn, Pb, Cu, and Cd) showed similar and significant effects on soil bacterial communities. Our findings provide new clues for reassessing the environmental risks of HMs in soils with different land use.

Draft Genome Sequence of Massilia sp. Strain ONC3, a Novel Bacterial Species of the Oxalobacteraceae Family Isolated from Garden Soil

From garden soil, we isolated and sequenced Massilia sp. strain ONC3, a new member of the Oxalobacteraceae within the Massilia genus. Sequence analysis showed an assembled genome size of 5,622,601 bp, with a predicted total of 5,104 protein-coding sequences, 3,194 functionally assigned genes, 2 rRNA operons, and 56 tRNAs.

From garden soil, we isolated and sequenced Massilia sp. strain ONC3, a new member of the Oxalobacteraceae within the Massilia genus. Sequence analysis showed an assembled genome size of 5,622,601 bp, with a predicted total of 5,104 protein-coding sequences, 3,194 functionally assigned genes, 2 rRNA operons, and 56 tRNAs.

Monitoring the Activated Sludge Activities Affected by Industrial Toxins via an Early-Warning System Based on the Relative Oxygen Uptake Rate (ROUR) Index

Shock load from industrial wastewater is known to harm the microbial activities of the activated sludge in wastewater treatment plants (WWTPs) and disturb their performance. This study developed a system monitoring the activated sludge activities based on the relative oxygen uptake rate (ROUR) and explored the influential factors with wastewater and the activated sludge samples collected from a typical WWTP in the Taihu Lake of southern Jiangsu province, China. The ROUR was affected by the concentration of toxic substances, mixed liquid suspended solids (MLSS), hydraulic retention time (HRT) and pH. Higher toxin contents significantly decreased the ROUR and the EC50 value of Zn2+, Ni2+, Cr(VI), Cu2+, and Cd2+ was 13.40, 15.54, 97.56, 12.01, and 14.65 mg/L, respectively. The ROUR declined with the increasing HRT and MLSS above 2000 mg/L had buffering capacities for the impacts of toxic substances to some extent. The ROUR remained stable within a broad range pH (6–10), covering most of the operational pH in WWTPs and behaving as an appropriate indicator for monitoring the shock load. A toxicity model assessing and predicting the ROUR was developed and fitted well with experimental data. Coupling the ROUR monitoring system and toxicity model, an online early-warning system was assembled and successfully used for predicting the toxicity of different potential toxic metals. This study provides a new universal toxicity model and an online early-warning system for monitoring the shock load from industrial wastewater, which is useful for improving the performance of WWTPs.

Massilia neuiana sp. nov., isolated from wet soil

A novel aerobic, Gram-stain-negative, rod-shaped, motile bacterium, strain PTW21^T, was isolated from wet soil. 16S rRNA gene sequence phylogenetic analysis of strain PTW21^T revealed an affiliation to the genus Massilia and it shared 98.5 and 98.1 % similarity with Massilianiastensis 5516 S-1^T and Massilia tieshanensis TS3^T, respectively. Growth occurred at 10-45 °C, pH 4.5-12.5 and NaCl concentrations up to 2 % (w/v). The major fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. The predominant respiratory quinone was Q-8. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain PTW21^T was 64.6 mol%. The results of DNA-DNA hybridization revealed that strain PTW21^T showed 37.4 % relatedness with Massilia niastensis 5516 S-1^T and 40.0 % with M. tieshanensis TS3^T. Based on phenotypic, chemotaxonomic and phylogenetic differences, strain PTW21^T (=CICC 24113^T=BCRC 81061^T) is proposed as the type strain of novel species of the genus Massilia with the names Massilia neuiana sp. nov.

Massilia buxea sp. nov., isolated from a rock surface

A Gram-stain-negative, rod-shaped and motile bacterial strain, designated A9^T, was isolated from the surface of rock collected from the shore of Nvshan lake in Mingguang, Anhui province, China. Phylogenetic analysis based on 16S rDNA sequence data showed that strain A9^T was affiliated with the genus Massilia and showed the highest sequence similarities to Massilia plicata KCTC 12344^T (98.8 %) and Massilia lurida CGMCC 1.10822^T (97.9 %). The major fatty acids (>5 %) were summed feature 3 (C16 : 1ω7c and/or C15 : 0 iso 2-OH), C16 : 0 and C18 : 1ω7c. Strain A9^T contained Q-8 as the predominant ubiquinone and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid as the predominant polar lipids. The DNA G+C content was 69.9 mol%. Mean DNA-DNA relatedness values between strain A9^T and its closest phylogenetic relatives, M. plicata KCTC 12344^T and M. lurida CGMCC 1.10822^T, were 38.8 % and 23.23 %, respectively. On the basis of the results obtained in this study, strain A9^T is considered to represent a novel species of the genus Massilia, for which the name Massilia buxea sp. nov. is proposed. The type strain is A9^T (=DSM 103547^T=CGMCC 1.15931^T=KCTC 52429^T).

Massilia phosphatilytica sp. nov., a phosphate solubilizing bacteria isolated from a long-term fertilized soil

A Gram-stain-negative and rod-shaped bacterial strain, 12-OD1T, with rock phosphate solubilizing ability was isolated from agricultural soil in Hailun, Heilongjiang, PR China. The isolate was affiliated to the genus Massilia, based on 16S rRNA gene sequence alignments, having the highest similarities with Massilia putida6 NM-7T (98.67 %), Massilia kyonggiensis TSA1T (98.28 %), and Massilia norwichensis NS9T (98.07 %), respectively. The DNA G+C content was 67.72 mol% and DNA-DNA hybridization showed low relatedness values (less than 47 %) between strain 12-OD1T and other phylogenetically related species of the genus Massilia. The predominant isoprenoid quinone was Q-8 and the polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were C17 : 0 cyclo (25.4 %), C16 : 0 (23.4 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1 ω6c) (22.5 %), which differentiates it from close relatives within the genus Massilia. Combined genetic, physiological and biochemical properties indicate that strain 12-OD1T is a novel species of the genus Massilia, for which the name Massilia phosphatilytica sp. nov., is proposed, with the type strain 12-OD1T (=CCTCC AB 2016251T=LMG 29956T=KCTC 52513T).

Bacillus iocasae sp. nov., isolated from Pacmanus hydrothermal field, Manus Basin

A novel bacterial strain S36T was isolated from the deep-sea sediment collected from Pacmanus hydrothermal field, Manus Basin. The strain was Gram-stain-positive, aerobic, rod-shaped, endospore-forming, and motile. It was able to grow at 16-50 °C, pH 6.0-10.0, and in the presence of 0-11 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain S36T was a member of genus Bacillus and shares the highest sequence identity with Bacillus herbersteinensis D-1,5aT (97.0 %). The value of DNA-DNA hybridization between strain S36T and B. herbersteinensis D-1,5aT was 22.8 %. The cell wall diagnostic diamino acid of strain S36T was meso-diaminopimelic acid and the polar lipid profile of strain S36T contained diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The predominant respiratory quinine was MK-7. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The genomic DNA G+C content of strain S36T was 43.0 mol%. On the basis of phylogenetic analysis, DNA-DNA hybridization, and phenotypic characteristics, it was concluded that strain S36T represents a novel species of the genus Bacillus, for which the name Bacillus iocasae sp. nov. was proposed. The type strain is S36T (=KCTC 33864T=DSM 104297T=CGMCC 1.16030T).

Massilia agri sp. nov., isolated from reclaimed grassland soil

A light yellow-coloured, Gram-stain-negative, motile and rod-shaped bacterium, designated strain K-3-1T, was isolated from reclaimed grassland soils of Belbari, Morang, Nepal. It was able to grow at 4-45 °C, at pH 5.0-10.0, and at 0-2 % (w/v) NaCl concentrations. This strain was taxonomically characterized by a polyphasic approach. Based on the 16S rRNA gene sequence analysis, strain K-3-1T belongs to the genus Massilia and is closely related to Massilia consociata CCUG 58010T (98.3 % sequence similarity), Massilia tieshanensis TS3T (98.1 % sequence similarity), Massilia kyonggiensis TSA1T (98.1 % sequence similarity), Massilia yuzhufengensisY1243-1T (98.1 % sequence similarity), Massilia haematophila CCUG 38318T (98.0 % sequence similarity), Massilia varians CCUG 35299T (97.9 % sequence similarity), Massilia niastensis 5516 S-1T (97.6 % sequence similarity) and Massilia alkalitolerans YIM 31775T (97.5 % sequence similarity). The predominant respiratory quinone was ubiquinone-8. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The predominant fatty acids of strain K-3-1T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, C12 : 0, C10 : 0 3-OH and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The genomic DNA G+C content of this novel strain was 66.8 mol%. The DNA-DNA relatedness between strain K-3-1T and its closest reference strains were significantly lower than the threshold value of 70 %. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain K-3-1T represents a novel species of the genus Massilia, for which the name Massilia agri sp. nov. is proposed. The type strain is K-3-1T (=KEMB 9005-446T=KACC 19000T=JCM 31661T).

Massilia psychrophila sp. nov., isolated from an ice core

A Gram-stain-negative, aerobic, rod-shaped, motile bacterium, strain B1555-1T, was isolated from an ice core drilled from Ulugh Muztagh Glacier, China. The optimum growth temperature of strain B1555-1T was 15 °C and optimum pH was 7. The major fatty acids of strain B1555-1T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The predominant respiratory quinone was Q-8. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain B1555-1T was 66.0 mol%. In 16S rRNA gene sequence comparisons, strain B1555-1T was affiliated to the genus Massilia and shared 98.30 and 97.13 % similarity with Massilia eurypsychrophila B528-3T and Massilia niabensis 5420S-26T, respectively. The results of DNA-DNA hybridization revealed that strain B1555-1T showed 49.8 % relatedness with M. eurypsychrophila B528-3T and 38.5 % with M. niabensis 5420S-26T. Based on the genotypic and phenotypic evidence presented in this study, strain B1555-1T represents a novel species of the genus Massilia, for which the name Massilia psychrophila sp. nov. is proposed. The type strain is B1555-1T (=CGMCC 1.15196T=JCM 30813T).