Mangrove Sediment Samples Research Articles

ECOLOGICAL INDICATOR AGENTS FOR INORGANIC CONTAMINANTS STATE MONITORING THROUGH SONNERATIA ALBA, AVICENNIA ALBA AND RHIZOPHORA APICULATA

Mangrove forest ecosystems are threatened by direct impacts such as cutting and pollution due to agricultural, industrialization and urbanization activities. Mangrove forests are often regarded as unpleasant environments with little intrinsic value. Mangrove forests perform valued regional and site-specific functions. Mangrove species can take up excessive nutrients and also play a crucial role in creating a favourable environment for a variety of chemical, biological and physical processes that contribute to the inorganic removal and degradation of organic compounds. Among the many mangrove species, Sonneratia alba, Avicennia alba and Rhizophora apiculata have been studied for biomonitoring of toxic heavy metals elements (Fe, Cu, Zn, Pb and Mn) in a wide range of plant tissues (roots and leaves) and sediment composition at three different locations in Negeri Sembilan, west coast of Malaysia. The results established that there were significant differences between the three mangrove species, locations, plant tissues and sediment samples and their interaction for all the five heavy metals content. The findings revealed that leaf tissues for all species accumulated mostly Fe, Zn, Pb and Cu. Interestingly we noticed that different localities will accumulate different type of heavy metals, for instance R. apiculata leaf tissues were detected with higher concentration of Cu and Pb at Kampung Sungai Sekawang whereas in another two sites were detected with Cu, Fe, Zn and Pb. S. alba indicated that the most heavy metals highly accumulated was Zn followed by Pb and Cu at Pasir Panjang. In this study A. alba showed Zn was highly accumulated in leaf tissues at Pasir Panjang. Thus, those three mangrove species appear to have the greatest potential for use as an effective ecological indicator tools as green application for inorganic contaminants monitoring in mangrove ecosystems.

Erythrobacter luteus sp. nov., isolated from mangrove sediment.

A Gram-staining-negative, orange-pigmented, aerobic bacterial strain, designated KA37T, was isolated from a mangrove sediment sample collected from Yunxiao mangrove National Nature Reserve, Fujian Province, China. Growth was observed at 4-37 °C, 0-3% (w/v) NaCl and pH 5-10. Mg2+ ions were required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus Erythrobacter, which belongs to the family Erythrobacteraceae. Strain KA37T was most closely related to Erythrobacter gangjinensis KCTC 22330T (96.9% sequence similarity), followed by Erythrobacter marinus KCTC 23554T (96.8%); similarity to other members of the genus was below 96.6%. The major fatty acids were C17 : 1ω6c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Strain KA37T did not produce bacteriochlorophyll a. The predominant respiratory quinone was ubiquinone 10 (Q-10). The polar lipids of strain KA37T were sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, five unknown lipids and one unidentified phospholipid. According to its morphology, physiology, fatty acid composition and 16S rRNA sequence, the novel strain most appropriately belongs to the genus Erythrobacter, but can be distinguished readily from species of the genus Erythrobacter with validly published names. The name Erythrobacter luteus sp. nov. is proposed, with strain KA37T ( = MCCC 1F01227T = KCTC 42179T) as the type strain.

Phaeobacterium nitratireducens gen. nov., sp. nov., a phototrophic gammaproteobacterium isolated from a mangrove forest sediment sample

A novel brown-coloured, Gram-negative-staining, rod-shaped, motile, phototrophic, purple sulfur bacterium, designated strain AK40T, was isolated in pure culture from a sediment sample collected from Coringa mangrove forest, India. Strain AK40T contained bacteriochlorophyll a and carotenoids of the rhodopin series as major photosynthetic pigments. Strain AK40T was able to grow photoheterotrophically and could utilize a number of organic substrates. It was unable to grow photoautotrophically and did not utilize sulfide or thiosulfate as electron donors. Thiamine and riboflavin were required for growth. The dominant fatty acids were C12 : 0, C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The polar lipid profile of strain AK40T was found to contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and eight unidentified lipids. Q-10 was the predominant respiratory quinone. The DNA G+C content of strain AK40T was 65.5 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represented a member of the family Chromatiaceae within the class Gammaproteobacteria. 16S rRNA gene sequence analysis indicated that strain AK40T was closely related to Phaeochromatium fluminis, with 95.2% pairwise sequence similarity to the type strain; sequence similarity to strains of other species of the family was 90.8-94.8%. Based on the sequence comparison data, strain AK40T was positioned distinctly outside the group formed by the genera Phaeochromatium, Marichromatium, Halochromatium, Thiohalocapsa, Rhabdochromatium and Thiorhodovibrio. Distinct morphological, physiological and genotypic differences from previously described taxa supported the classification of this isolate as a representative of a novel species in a new genus, for which the name Phaeobacterium nitratireducens gen. nov., sp. nov. is proposed. The type strain of Phaeobacterium nitratireducens is AK40T ( = JCM 19219T = MTCC 11824T).

Rhodovulum mangrovi sp. nov., a phototrophic alphaproteobacterium isolated from a mangrove forest sediment sample.

A novel Gram-staining-negative, purple non-sulfur bacterium, strain AK41(T), was isolated from a sediment sample collected from Coringa mangrove forest, Andhra Pradesh, India. A red-brownish-coloured culture was obtained on modified Pfennig medium after enrichment with 2 % NaCl and 0.3 % pyruvate under 2000 lx illumination. Individual cells were ovoid-rod-shaped and non-motile. Bacteriochlorophyll a and carotenoids of the spheroidene series were present as photosynthetic pigments. Strain AK41(T) was halophilic and grew photoheterotrophically with a number of organic compounds as carbon sources and electron donors. It was unable to grow photoautotrophically. It did not utilize sulfide or thiosulfate as electron donors. The fatty acids were found to be dominated by C16 : 0 and C18 : 1ω7c. Strain AK41(T) contained phosphatidylglycerol, phosphatidylethanolamine, an unknown aminolipid and four unknown lipids as polar lipids. Q-10 was the predominant respiratory quinone. The DNA G+C content of strain AK41(T) was 68.9 mol%. 16S rRNA gene sequence analysis indicated that strain AK41(T) was a member of the genus Rhodovulum and was closely related to Rhodovulum sulfidophilum, with 96.0 % similarity to the type strain; the 16S rRNA gene sequence similarity to the type strains of other species of the genus Rhodovulum was 93.9-95.8 %. Phylogenetic analyses indicated that strain AK41(T) clustered with the type strains of Rhodovulum marinum, Rdv. kholense, Rdv. sulfidophilum and Rdv. visakhapatnamense with sequence similarity of 95.9-96.2 %. Based on data from the current study, strain AK41(T) is proposed to represent a novel species of the genus Rhodovulum, for which the name Rhodovulum mangrovi sp. nov. is proposed. The type strain of Rhodovulum mangrovi is AK41(T) ( = MTCC 11825(T) = JCM 19220(T)).

Biodegradation of carcinogenic textile azo dyes using bacterial isolates of mangrove sediment

Objective: To evaluate the biodegrading property against carcinogenic azo dyes using bacterial isolates of mangrove sediment. Methods: The bacterial isolates were subjected to submerged fermentation and their growth kinetics were studied. The potential strain was characterized using 16S rDNA sequencing. Results: In the present study, dye degrading bacterial colonies were isolated from the mangrove sediment samples of Parangipettai estuarine area, Tamil Nadu. Of the 30 morphologically different strains isolated, 5 showed antagonistic property. The growth kinetics of the two strains, P1 and G1, which showed potent activity were calculated. One particular isolate (P1) showing promising dye degrading potential in the submerged fermentation was further characterized. The strain was identified as Paenibacillus sp. by 16S rDNA sequencing. Conclusions: This study reveals the less explored microflora of mangrove sediments. The novel strain may further be analyzed and used in the treatment of effluent from dye industry so as to reduce the impact of carcinogenic contaminants.

Mangrovibacterium diazotrophicum gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from a mangrove sediment, and proposal of Prolixibacteraceae fam. nov.

A nitrogen-fixing bacterium, designated strain SCSIO N0430(T), was isolated from a mangrove sediment sample. Analysis of the sequence of the nifH gene responsible for nitrogen fixation in this strain indicated a close relationship to an uncultured bacterium ZNZ-D11 (GenBank accession no. JF896696). 16S rRNA gene sequence analysis revealed that this isolate had less than 93 % similarity to its closest relative, Sunxiuqinia elliptica DQHS4(T). A phylogenetic tree reconstructed based on 16S rRNA gene sequences revealed that strain SCSIO N0430(T) was a member of the phylum Bacteroidetes. Chemotaxonomic and physiological characteristics, including phospholipids and major fatty acids, readily distinguished the isolate from established members of the phylum Bacteroidetes. It is concluded that strain SCSIO N0430(T) represents a novel genus and species, for which the name Mangrovibacterium diazotrophicum gen. nov., sp. nov. is proposed, with the type strain of the species SCSIO N0430(T) ( = KCTC 32129(T) = DSM 27148(T) = JCM 19152(T)). Based on phylogenetic characteristics and 16S rRNA gene signature nucleotide patterns, the three genera Sunxiuqinia, Prolixibacter and Mangrovibacterium are proposed to make up a novel family, Prolixibacteraceae fam. nov., in the order Bacteroidales.

Tropical Aquatic Archaea Show Environment-Specific Community Composition

The Archaea domain is ubiquitously distributed and extremely diverse, however, environmental factors that shape archaeal community structure are not well known. Aquatic environments, including the water column and sediments harbor many new uncultured archaeal species from which metabolic and ecological roles remain elusive. Some environments are especially neglected in terms of archaeal diversity, as is the case of pristine tropical areas. Here we investigate the archaeal composition in marine and freshwater systems from Ilha Grande, a South Atlantic tropical environment. All sampled habitats showed high archaeal diversity. No OTUs were shared between freshwater, marine and mangrove sediment samples, yet these environments are interconnected and geographically close, indicating environment-specific community structuring. Group II Euryarchaeota was the main clade in marine samples, while the new putative phylum Thaumarchaeota and LDS/RCV Euryarchaeota dominated freshwaters. Group III Euryarchaeota , a rare clade, was also retrieved in reasonable abundance in marine samples. The archaeal community from mangrove sediments was composed mainly by members of mesophilic Crenarchaeota and by a distinct clade forming a sister-group to Crenarchaeota and Thaumarchaeota. Our results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria.

Draft Genome Sequence of Streptomyces gancidicus Strain BKS 13-15

We report the 7.3-Mbp genome sequence of Streptomyces gancidicus strain BKS 13-15, isolated from mangrove sediment samples collected from the Bhitar Kanika Mangrove Reserve Forest, Odissha, India. The draft genome of strain Streptomyces gancidicus strain BKS 13-15 consists of 7,300,479 bp with 72.6% G+C content, 6,631 protein-coding genes, and 71 RNAs.

Mangrovimonas yunxiaonensis gen. nov., sp. nov., isolated from mangrove sediment

A Gram-negative, short-rod-shaped, orange-pigmented bacterium, strain LYYY01(T), was isolated from a mangrove sediment sample collected from Yunxiao mangrove National Nature Reserve, Fujian Province, China. 16S rRNA gene sequence comparisons showed that strain LYYY01(T) is a member of the family Flavobacteriaceae, forming a distinct lineage with species of the genera Meridianimaribacter, Sediminibacter, Gelidibacter and Subsaximicrobium. The 16S rRNA gene sequence similarity between strain LYYY01(T) and the type strains of related species ranged from 93.9 to 90.9%. Growth was observed at temperatures from 10 to 38 °C, at salinities from 1 to 7% and at pH from 6 to 10. The DNA G+C content of the strain was 38.6 mol% and the major respiratory quinone was menaquinone-6 (MK-6). The major fatty acids were iso-C15:1 (27.6%), iso-C15:0 (24.0%), iso-C17:0 3-OH (12.0%) and iso-C16:0 3-OH (6.2%). According to its morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain LYYY01(T) is considered to represent a novel species of a new genus in the family Flavobacteriaceae, for which the name Mangrovimonas yunxiaonensis gen. nov., sp. nov. is proposed. The type strain of Mangrovimonas yunxiaonensis is LYYY01(T) (=CGMCC 1.12280(T)=LMG 27142(T)).

Denaturing Gradient Gel Electrophoresis and Barcoded Pyrosequencing Reveal Unprecedented Archaeal Diversity in Mangrove Sediment and Rhizosphere Samples

Mangroves are complex ecosystems that regulate nutrient and sediment fluxes to the open sea. The importance of bacteria and fungi in regulating nutrient cycles has led to an interest in their diversity and composition in mangroves. However, very few studies have assessed Archaea in mangroves, and virtually nothing is known about whether mangrove rhizospheres affect archaeal diversity and composition. Here, we studied the diversity and composition of Archaea in mangrove bulk sediment and the rhizospheres of two mangrove trees, Rhizophora mangle and Laguncularia racemosa, using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing of archaeal 16S rRNA genes with a nested-amplification approach. DGGE profiles revealed significant structural differences between bulk sediment and rhizosphere samples, suggesting that roots of both mangrove species influence the sediment archaeal community. Nearly all of the detected sequences obtained with pyrosequencing were identified as Archaea, but most were unclassified at the level of phylum or below. Archaeal richness was, furthermore, the highest in the L. racemosa rhizosphere, intermediate in bulk sediment, and the lowest in the R. mangle rhizosphere. This study shows that rhizosphere microhabitats of R. mangle and L. racemosa, common plants in subtropical mangroves located in Rio de Janeiro, Brazil, hosted distinct archaeal assemblages.

Agromyces indicus sp. nov., isolated from mangroves sediment in Chorao Island, Goa, India

A Gram-positive, non-motile, rod-shaped bacterium strain NIO-1018(T) isolated from a mangrove sediment sample of the Chorao Island, Goa, India, was subjected to a detailed polyphasic taxonomic study. The strain designated as NIO-1018(T) matched with most of the phenotypic and chemotaxonomic properties of the genus Agromyces and represents a novel species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NIO-1018(T) fell within the cluster comprising species of the genus Agromyces, clustering with Agromyces soli (98.1 %), Agromyces flavus (97.9 %), Agromyces aurantiacus (97.7 %) and Agromyces ulmi (97.3 %). The predominant menaquinone was MK-12, and the major cellular fatty acids were anteiso-C(15:0), iso-C(16:0), anteiso-C(17:0) and iso-C(15:0). The polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content of strain NIO-1018(T) was 71.8 mol%. The combination of phylogenetic analysis, DNA-DNA relatedness, phenotypic characteristics and chemotaxonomic data supported the view that strain NIO-1018(T) represents a novel species of the genus Agromyces, for which the name Agromyces indicus sp. nov. is proposed. The type strain is NIO-1018 (=JCM 17573(T) = CCTCC AB2011122(T)).

Mangrove sediment, a new source of potential biosurfactant-producing bacteria

Biosurfactant-producing bacteria were isolated from mangrove sediment samples collected in the southern part of Thailand by an enrichment-culture technique in which lubricating oil was the sole carbon source. A total of 1,600 colonies were obtained, which were screened for biosurfactant production using the qualitative drop-collapsing test in a mineral salts medium containing 1% of different carbon sources (commercial sugar, glucose, molasses, and used lubricating oil). Ninety-five isolates were positive for biosurfactant production based on the results of this test, among which 20 could reduce the surface tension of the 48-h culture supernatant. The phylogenetic position of these 20 isolates was evaluated by 16S rRNA gene sequence analysis. The production of biosurfactants was determined for strains representative of eight different bacterial genera. Leucobacter komagatae 183, one of the newly isolated strains showing biosurfactant production, produced extracellular biosurfactants which reduced the surface tension of the culture supernatant from 72.0 to 32.0 m/Nm. Eighteen strains released extracellular emulsifiers able to stabilize the emulsion formed. Among these, the strains L. komagatae 183 and Ochrobactrum anthropi 11/6 exhibited emulsification activities comparable to those of synthetic surfactants. Overall, the new biosurfactant-producing strains isolated in this study display promising features for the future development and use in economically efficient industrial-scale biotechnological processes.

Micromonospora haikouensis sp. nov., isolated from mangrove soil

An actinomycete strain 232617(T) was isolated from a composite mangrove sediment sample collected in Haikou, China. Phylogenetic analysis of the 16S rRNA gene sequence of strain 232617(T) indicated the highest similarity with Micromonospora siamensis TT2-4(T) (99.05%), Micromonospora krabiensis A-2(T) (98.99%) and Micromonospora carbonacea DSM 43815(T) (98.91%). The gyrB gene sequence analysis also indicated that 232617(T) should be assigned to the genus Micromonospora. The cell wall contains meso-DAP and glycine. The major menaquinones were MK-10(H(4)) and MK-10(H(6)), with MK-9(H(4)) as minor components. The characteristic whole-cell sugars are xylose, arabinose and glucose. The phospholipid profile comprises phosphatidylethanolamine, diphosphatidlglycerol and phosphatidylinositol mannoside. The DNA G+C content is 71.5mol%. Furthermore, a combination of DNA-DNA relatedness and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from the closest related species. On the basis of these phenotypic and genotypic data, strain 232617(T) represents a novel species of the genus Micromonospora, for which the name Micromonospora haikouensis sp. nov. is proposed. The type strain is 232617(T) (=CCTCC AA 201112 (T)=DSM 45626 (T)).

Trace Metals Concentrations in Mangrove Sediments of Sepetiba Bay (Rio de Janeiro, Brazil): Microwave Assisted Digestion with Nitric Acid and Aqua Regia

Mangrove sediments have a great capacity to accumulate trace metals that can be remobilized thus contaminating the water and biota. Concentrations of trace metals (Cu, Ni, Pb and Zn) in mangrove sediment samples from Sepetiba Bay (Brazil) determined using two different protocols were compared, in order to give support for the establishment of a future legislation of environmental assessment of sediment quality in Brazil. Surface sediment samples were collected in three mangrove forests of Sepetiba Bay and were analyzed to determine pH, Eh, salinity, and the percentages of sand, silt, clay, total organic carbon (TOC), total N and total P. Concentrations of Cu, Ni, Pb and Zn were determined using two microwave acid digestion protocols, with two different agents: nitric acid (HNO3) and aqua regia (HCl/HNO3). Results showed that the choice of the digestion method to use in the evaluation of environmental contamination and monitoring of trace metals in sediments should be made carefully, taking into account their physical and chemical characteristics in order to avoid misclassification of environmental impacts.

Desulfobaculum xiamenensis gen. nov., sp. nov., a member of the family Desulfovibrionaceae isolated from marine mangrove sediment

A taxonomic study was carried out on strain P1(T), which was isolated from mangrove sediment samples collected from Qinglan Port (Hainan, China). Cells were curved rods, that were motile, with a single polar flagellum. The strain was non-spore-forming with a cell size of 0.6×1.5-2.2 µm. Catalase and oxidase activities were not detected. Growth was observed in the temperature range 22-44 °C (optimum, 35-40 °C) and pH range 5.5-8.5 (optimum, pH 7.0). NaCl was required for growth and tolerated at up to 3.5% (w/v) (optimum, 0.5%). Strain P1(T) utilized hydrogen, succinate, L-malate, citrate, oxalate, DL-lactate, pyruvate, or cysteine as electron donors, and sulfate or sulfite as electron acceptors. Fermentation products from pyruvate were acetate, H(2) and CO(2). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain P1(T) formed a distinct evolutionary lineage within the family Desulfovibrionaceae. Strain P1(T) was most closely related to members of the genera Desulfovibrio (92.0-94.3% 16S rRNA gene sequence similarity), Desulfocurvus (91.1%), Bilophila (87.9%) and Lawsonia (86.0%) of the family Desulfovibrionaceae. The DNA G+C content of strain P1(T) was 64.5 mol% and the major cellular fatty acids were iso-C(15:0) (18.8%), anteiso-C(15:0) (5.0%), C(16:0) (14.2%) and iso-C(17:1)ω9c (24.4%). The predominant menaquinone was MK-7 (97%). Major polar lipids were phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Strain P1(T) was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of the phenotypic and phylogenetic data, strain P1(T) represents a novel species of a new genus, for which the name Desulfobaculum xiamenensis gen. nov., sp. nov. is proposed. The type strain of Desulfobaculum xiamenensis is P1(T) (=CGMCC 1.5166(T)=DSM 24233(T)).

Actinomadura sediminis sp. nov., a marine actinomycete isolated from mangrove sediment

In this study, the taxonomic position of an actinobacterium, strain YIM M 10931(T), which was isolated from a mangrove sediment sample collected in Dugong Creek, Little Andaman, India, was determined by a polyphasic approach. This gram-positive, aerobic strain produced branched substrate mycelium and aerial hyphae, which differentiated into short, hooked or spiral spore chains. The organism contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The whole cell sugars consisted of mannose, ribose, glucose, galactose and madurose. The cellular fatty acid profile mainly consisted of iso-C(16 : 0), 10-methyl C(18 : 0) and C(16 : 0). The quinone system was predominantly composed of MK-9(H(8)) (45.5 %) and MK-9(H(6)) (39 %). The phospholipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol and two unknown phospholipids. The organism showed a combination of morphological and chemotaxonomic properties typical of members of the genus Actinomadura. Moreover, phylogenetic analysis based on a 16S rRNA gene sequence generated from the strain identified its closest relatives as Actinomadura cremea DSM 43676(T) (98.4 % sequence similarity), Actinomadura rifamycini DSM 43936(T) (97.4 %) and Actinomadura apis IM17-1(T) (96.9 %). It was obvious from the resulting phylogenetic trees that strain YIM M 10931(T) belongs to a distinct subclade within the evolutionary radiation of the genus Actinomadura. DNA-DNA hybridizations of strain YIM M 10931(T) with A. cremea DSM 43676(T) and A. rifamycini DSM 43936(T) were performed and further confirmed that the isolate represents a separate genomic species. Based on the phenotypic and genotypic characteristics presented, it is proposed that strain YIM M 10931(T) represents a novel species within the genus Actinomadura, for which the name Actinomadura sediminis sp. nov. is proposed; the type strain is YIM M 10931(T) ( = CCTCC AA 2010009(T) = DSM 45500(T)).

Kazachstania bromeliacearum sp. nov., a yeast species from water tanks of bromeliads

Cultures of a novel nutritionally specialized, fermentative yeast species were isolated from 34 water tanks of five bromeliad species, two mangrove sediment samples and one swamp water sample in Rio de Janeiro, Brazil. Sequence analysis of the D1/D2 domains of the large subunit of the rRNA gene showed that the novel species belongs to the genus Kazachstania. The novel species differs from Kazachstania martiniae by 11 substitutions and 2 gaps in the sequence of the domains D1/D2 of the LSU rRNA gene. The name Kazachstania bromeliacearum sp. nov. is proposed for the novel species. The type strain is IMUFRJ 51496T (=CBS 7996T=DBVPG 6864T=UFMG BR-174T).

Integrated lysis procedures reduce extraction biases of microbial DNA from mangrove sediment

Sufficient lysis of soil or sediment microbes is a critical step for analyzing microbial community structures and for preparing metagenomic DNA libraries. The present study compared lysis methods for recovering archaeal, bacterial, actinomycete, and fungal DNAs from a mangrove sediment sample. PCR results showed that individual procedures using SDS, lysozyme, sonication, freeze-thaw, microwave, and vigorous shaking could extract archaeal or bacterial DNA but failed for actinomycetes or fungi cells. In comparison, an integrated lysis procedure using SDS, lysozyme, and vigorous shaking successfully obtained fungal DNA, and a combination of SDS, lysozyme, vigorous shaking, and microwave treatments recovered DNA from actinomycetes. Denaturing gradient gel electrophoresis (DGGE) results showed that although single lysis procedures can lyse bacterial DNA, all of them assessed the indigenous bacterial community structure with significant biases. The integrated lysis protocols described in the present study could be useful for extracting DNA from various types of sediments.

Verrucosispora lutea sp. nov., isolated from a mangrove sediment sample

A novel Gram-positive, aerobic, spore-forming actinobacterium, designated strain YIM 013T, was isolated from a mangrove sediment sample and subjected to a polyphasic taxonomic study. The peptidoglycan type was A1gamma and the major whole-cell sugars contained glucose and xylose. The phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and some unknown phospholipids. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C15:0 and iso-C16:0. The genomic DNA G+C content was 69.3 mol%. blast search results based on an almost-complete 16S rRNA gene sequence showed that strain YIM 013T had the highest similarity with Verrucosispora gifhornensis DSM 44337T (98%) and phylogenetic analysis revealed that strain YIM 013T should be assigned to the genus Verrucosispora. The mean level of DNA-DNA relatedness between strain YIM 013T and V. gifhornensis DSM 44337T was 38.2%. Based on its phenotypic and genotypic characteristics, strain YIM 013T (=CCTCC AA207012T=KCTC 19195T) is proposed to be the type strain of a novel species, Verrucosispora lutea sp. nov.

Diversity of methanogenic archaea in a mangrove sediment and isolation of a newMethanococcoidesstrain

Mangrove forest sediments produce significant amounts of methane, but the diversity of methanogenic archaea is not well known at present. Therefore, 16S rRNA gene libraries were made using archaea-specific primers and DNA extracted directly from Tanzanian mangrove sediment samples as a template. Analysis of sequence data showed phylotypes closely related to cultivated methylotrophic methanogenic archaea from the marine environment, or distantly related to acetoclastic and hydrogenotrophic methanogenic archaea. In an attempt to isolate relevant methanogenic archaea, we succeeded in obtaining a new mesophilic methylotrophic methanogenic archaeon (strain MM1) capable of utilizing methanol and methylated amines as the only substrates. Under optimum conditions, the cells of strain MM1 exhibited a high specific growth rate (mu) of 0.21+/-0.03 (i.e. doubling time of 3.2 h) on both methanol and trimethylamine. The 16S rRNA gene sequence of strain MM1 clustered with five environmental clones, indicating that MM1 is an important methanogenic methylotroph in mangrove sediments. Based on physiological and phylogenetic analyses, strain MM1 is proposed to be included in the species of Methanococcoides methylutens.