Isolation of Thalassobius mangrovi sp. nov., a novel bacterium in the family Rhodobacteraceae, from marine mangrove sediment.

A Gram-stain-negative, strictly aerobic and oval-shaped bacterial strain with a flagellum, designated GS-10T, was isolated from mangrove wetland sediment. GS-10T grew at 20-40 °C (optimum, 37 °C), in the pH range of 5.0-11.0 (optimum, 6.0-8.0) and under various NaCl concentrations from 1 to 11 % (w/v) (optimum, 5-6 %). The respiratory quinone was ubiquinone-10, and the predominant polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids (>10 % of the total fatty acids) were summed feature 4 (C17 : 1iso I/anteiso B) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The G+C content of the genomic DNA was 63.71 %. On the basis of the results from comparative analysis of the 16S rRNA gene sequence, GS-10T represents a member of the family Rhodobacteraceae and had the highest sequence similarity to Thalassobius gelatinovorus CECT 4357T (97.47 %), followed by Lutimaribacter pacificus W11-2BT (97.03 %), Marivita cryptomonadis CL-SK44T (96.83 %), Thalassobius autumnalis CECT 5118T (96.75 %) and Thalassobius mediterraneus CECT 5383T (96.68 %). Phylogenetic trees based on 16S rRNA gene sequences, multilocus sequence analysis (MLSA) and whole genome sequences revealed that GS-10T clustered with species within the genus Thalassobius. The average nucleotide identity (ANI) and the average amino acid identity (AAI) values were calculated from complete genome sequences and indicated that GS-10T represented a novel species of the genus Thalassobius, and the name Thalassobius mangrovi sp. nov. is proposed for this species. The type strain of Thalassobius mangrovi is GS-10T (=MCCC 1K03624T=KCTC 82131T).

Nitrogen loss by anaerobic ammonium oxidation in a mangrove wetland of the Zhangjiang Estuary, China.

Anaerobic ammonium oxidation (anammox), a microbial process in which NH4+ is oxidized to N2 gas, is considered a significant nitrogen cycle process, but its significance in mangrove wetland sediments, particularly its depth- and genus-specific distribution and activity have remained uncertain. Here we report the vertical distribution, abundance, activity and role of anammox bacteria in mangrove sediments of Zhangjiang Estuary, China. We used stable isotope-tracer techniques, 16S rRNA and anammox bacterial functional gene (Hydrazine synthase B: hzsB) clone libraries and quantitative polymerase chain reaction (qPCR) assays, along with an assessment of nutrient profiles of sediment core samples. We observed a widespread occurrence of anammox bacteria at different depths of mangrove sediments. The abundance of anammox bacterial 16S rRNA and hzsB genes ranged from 0.41×107 to 9.74×107 and from 0.42×106 to 6.44×106 copies per gram of dry soil and peaked in the upper layer of mangrove sediments. We also verified the co-occurrence of different genera of anammox microorganisms in mangrove sediments, with Candidatus Scalindua and Candidatus Kuenenia being the dominant genera. Potential anammox rates ranged from 4.83 to 277.36 nmolN2·g-1·d-1 at different depths of sediment cores, and the highest rates were found in the deeper layer (70-100cm) of mangrove sediments. Scaling our findings up to the entire mangrove system, we estimated that anammox hotspots accounted for a loss of 751 gN·m-2·y-1, and contributed to over 12% of the nitrogen lost from the deeper layer of mangrove sediments in this region.

Sphingosinithalassobacter portus gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from surface seawater.

A Gram-stain-negative strain, designated FM6T, was isolated from surface seawater sampled at the port in Xiamen, PR China. Strain FM6T showed less than 96.3 % 16S rRNA gene sequence similarity to the type strains of species with validly published names. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FM6T belonged to the family Sphingomonadaceae and was closely related to species of the genera Sphingomonas (96.3 %) and Stakelama (96.0 %). Ubiquinone-10 was the predominant respiratory quinone. Cells were motile with a single polar flagellum. Growth occurred at temperatures from 20 to 45 °C (optimum, 30 °C), at pH values between pH 6.0 and 8.0 (optimum, pH 7.0) and in 0-4.0 % (w/v) NaCl (optimum, 1.0-1.5 %). Predominant polar lipids were sphingoglycolipid, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, five unidentified glycolipids and five unidentified polar lipids. The major fatty acids were summed feature 8 (containing C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content of the type strain was 63.8 mol%. On the basis of the results of phylogenetic analysis, combined with phenotypic and chemotaxonomic data, strain FM6T is considered to represent a novel species in a new genus in the family Sphingomonadaceae for which the name Sphingosinithalassobacter portus gen. nov., sp. nov. is proposed. The type strain of Sphingosinithalassobacter portus gen. nov., sp. nov. is FM6T (=MCCC 1K03501T=JCM 32714T).

Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China.

Microorganisms play important roles in mangrove ecosystems. However, we know little about the ecological implications of mangrove microbiomes for high productivity and the efficient circulation of elements in mangrove ecosystems. Here, we focused on mangrove sediments located at the Yunxiao National Mangrove Reserve in southeast China, uncovering the mangrove microbiome using the 16S rRNA gene and shotgun metagenome sequencing approaches. Physicochemical assays characterized the Yunxiao mangrove sediments as carbon (C)-rich, sulfur (S)-rich, and nitrogen (N)-limited environment. Then phylogenetic analysis profiling a distinctive microbiome with an unexpected high frequency of Chloroflexi and Nitrospirae appeared to be an adaptive characteristic of microbial structure in S-rich habitat. Metagenome sequencing analysis revealed that the metabolic pathways of N and S cycling at the community-level were routed through ammonification and dissimilatory nitrate reduction to ammonium for N conservation in this N-limited habitat, and dissimilatory sulfate reduction along with polysulfide formation for generating bioavailable S resource avoiding the biotoxicity of sulfide in mangrove sediments. In addition, methane metabolism acted as a bridge to connect C cycling to N and S cycling. Further identification of possible biogeochemical linkers suggested Syntrophobacter, Sulfurovum, Nitrospira, and Anaerolinea potentially drive the coupling of C, N, and S cycling. These results highlighting the adaptive routed metabolism flow, a previously undescribed property of mangrove sediment microbiome, appears to be a defining characteristic of this habitat and may significantly contribute to the high productivity of mangrove ecosystems, which could be used as indicators for the health and biodiversity of mangrove ecosystems.

Litorivita pollutaquae gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae isolated from surface seawater of Xiamen Port, China.

A Gram-stain-negative Rhodobacterales strain, designated as FSX-11T, was isolated from surface seawater of Xiamen port in China. Strain FSX-11T showed less than 96.5 % 16S rRNA gene sequence similarity to the type strains of species with validly published names. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel isolate formed a distinct monophyletic clade within the family Rhodobacteriaceae and clustered distantly with the genera Thalassobius and Marivita. Cells of strain FSX-11T were non-motile, oval-shaped and facultative anaerobic. Optimal growth occurred at 20-30 °C, at pH 7.0-8.0 and in the presence of 2-3 % NaCl (w/v). The major respiratory quinone was ubiquinone-10. Summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), 11-methyl C18 : 1ω7c and C16 : 0 were the major fatty acids. The DNA G+C content of strain FSX-11T was 58.7 mol%. On the basis of phylogenetic analysis, phenotypic and chemotaxonomic characteristics and 16S rRNA gene signature nucleotide patterns, strain FSX-11T represents a novel species in a novel genus within the family Rhodobacteraceae, for which the name Litorivita pollutaquae gen. nov., sp. nov. is proposed. The type strain is FSX-11T (=JCM 32715T=MCCC 1K03503T).

Molecular and stable isotopic evidence for the occurrence of nitrite-dependent anaerobic methane-oxidizing bacteria in the mangrove sediment of Zhangjiang Estuary, China.

Nitrite-dependent anaerobic methane oxidation (n-damo), which is mediated by "Candidatus Methylomirabilis oxyfera-like" bacteria, is unique in linking the carbon and nitrogen cycles. However, the niche and activity of n-damo bacteria in the mangrove ecosystem have not been confirmed. Here, we report the occurrence of the n-damo process in the mangrove wetland of the Zhangjiang Estuary, China. The widespread occurrence of n-damo bacteria in mangrove wetland was confirmed using real-time quantitative polymerase chain reaction (qPCR) assay, which showed that the abundance of Methylomirabilis oxyfera-like bacterial 16S rRNA and pmoA genes ranged from 2.43 × 106 to 2.09 × 107 and 2.07 × 106 to 3.38 × 107copies per gram of dry soil in the examined sediment cores. The highest amount of targeting genes was all detected in the upper layer (0-20 cm). Phylogenetic analyses of n-damo bacterial 16S rRNA and pmoA genes illustrated the depth-specific distribution and high diversity of n-damo bacteria in the mangrove wetland. Stable isotope experiments further confirmed the occurrence of n-damo in the examined mangrove sediments, and the potential n-damo rates ranged from 25.93 to 704.08 nmol CO2 per gram of dry soil per day at different depths of the sediment cores, with the n-damo being more active in the upper layer of the mangrove sediments. These results illustrate the existence of active M. oxyfera-like bacteria and indicate that the n-damo process is a previously overlooked microbial methane sink in the mangrove wetlands.