Synergistic effects of succession and microtopography of moraine on the fungal spatial diversity in a glacier forefield.

Primary succession and microtopography result in environmental changes and are important processes influencing the community assembly of soil fungi in the Arctic region. In glacier forefields that contain a series of moraine ridges, both processes contribute synchronously to fungal spatial diversity. To reveal the synergistic effects of succession and microtopography, we investigated the fungal community structure and environmental variables in the moraines of the Arklio Glacier, Ellesmere Island. The study sites were established at four locations from the top to the bottom of the ridge slope within each of the three moraine ridges of different post-glacial ages. The location-dependent community composition was equally diverse in both the initial and later stages of succession, suggesting that successional time could alter the effects of microtopography on the fungal community. Moreover, our results suggest that fungal communities at different locations follow different successional trajectories, even if they have passed through the same time lapse. Such a synergistic effect of succession and microtopography of moraines does not allow for parallel changes in fungal communities among moraines or among locations, suggesting that the moraine series contributes substantially to fungal spatial diversity in the glacier forefield.

Vegetation as a key driver of the distribution of microbial generalists that in turn shapes the overall microbial community structure in the low Arctic tundra.

Understanding the variability of microbial niches and their interaction with abiotic and biotic factors in the Arctic can provide valuable insights into microbial adaptations to extreme environments. This study investigates the structure and diversity of soil bacterial communities obtained from sites with varying vegetation coverage and soil biogeochemical properties in the low Arctic tundra and explores how bacteria interact under different environmental parameters. Our findings reveal differences in bacterial composition and abundance among three bacterial niche breadths (specialists, common taxa, and generalists). Co-occurrence network analysis revealed Rhizobiales and Ktedonobacterales as keystone taxa that connect and support other microbes in the habitat. Low-elevation indicators, such as vascular plants and moisture content, were correlated with two out of three generalist modular hubs and were linked to a large proportion of generalists' distribution (18%). Structural equation modeling revealed that generalists' distribution, which influenced the remaining microbial communities, was mainly regulated by vegetation coverage as well as other abiotic and biotic factors. These results suggest that elevation-dependent environmental factors directly influence microbial community structure and module formation through the regulation of generalists' distribution. Furthermore, the distribution of generalists was mainly affected by macroenvironment filtering, whereas the distribution of specialists was mainly affected by microenvironment filtering (species-engineered microbial niche construction). In summary, our findings highlight the strong top-down control exerted by vegetation on generalists' distribution, which in turn shapes the overall microbial community structure in the low Arctic tundra.

Aquariibacter albus gen. nov., sp. nov., a new member of the order Burkholderiales, isolated from a freshwater aquarium.

A novel bacterium, strain SJAQ100T, was isolated from a freshwater aquarium and was characterized taxonomically and phylogenetically. Strain SJAQ100T was a Gram-stain-negative, aerobic, rod-shaped and non-motile bacterium. The strain grew optimally with 0 % NaCl and at 25-37 °C on Reasoner's 2A agar. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strain SJAQ100T clustered with members of Burkholderiales incertae sedis in the order Burkholderiales, but sequence similarities to known species were less than 96.5 %. The genomic DNA G+C content of strain SJAQ100T was 71.2 mol%. Genomic comparisons of strain SJAQ100T with species in the order Burkholderiales were made using the Genome-to-Genome Distance Calculator, average nucleotide identity and average amino acid identity analyses (values indicated ≤22.1, ≤78.1, and ≤68.1 % respectively). Strain SJAQ100T contained C16 : 0 and C16 : 1 ω7c/C16 : 1 ω6c as major fatty acids and Q-8 as the major quinone. The major polyamines were putrescine and cadaverine. Strain SJAQ100T contained phosphatidylethanolamine and diphosphatidylglycerol as major polar lipids. Based on the genotypic, chemotaxonomic and phenotypic results, strain SJAQ100T represents a novel genus and species, Aquariibacter albus gen. nov., sp. nov., which belongs to order Burkholderiales and the class Betaproteobacteria. The type strain is SJAQ100T (=KCTC 72203T=CGMCC 1.18869T=MCC 4385T).

Distribution of Dimethylsulfoniopropionate Degradation Genes Reflects Strong Water Current Dependencies in the Sanriku Coastal Region in Japan: From Mesocosm to Field Study.

Dimethyl sulfide (DMS) is an important component of the global sulfur cycle as it is the most abundant sulfur compound that is emitted via the ocean surface to the atmosphere. Dimethylsulfoniopropionate (DMSP), the precursor of DMS, is mainly produced by phytoplankton and is degraded by marine bacteria. To reveal the role of bacteria in the regulation of DMSP degradation and DMS production, mesocosm and field studies were performed in the Sanriku Coast on the Pacific Ocean in northeast Japan. The responsible bacteria for the transformation of DMSP to DMS and the assimilation of DMSP were monitored, and the genes encoding DMSP lyase (dddD and dddP) and DMSP demethylase (dmdA) were analyzed. The mesocosm study showed that the dmdA subclade D was the dominant DMSP degradation gene in the free-living (FL) and particle-associated (PA) fractions. The dddD gene was found in higher abundance than the dddP gene in all the tested samples. Most importantly, DMS concentration was positively correlated with the abundance of the dddD gene. These results indicated that bacteria possessing dmdA and dddD genes were the major contributors to the DMSP degradation and DMS production, respectively. The genes dmdA subclade D and dddP were abundant in the Tsugaru Warm (TW) Current, while the dmdA subclade C/2 and dddD genes were dominant in the Oyashio (OY) Current. Functional gene network analysis also showed that the DMSP degradation genes were divided into OY and TW Current-related modules, and genes sharing similar functions were clustered in the same module. Our data suggest that environmental fluctuations resulted in habitat filtering and niche partitioning of bacteria possessing DMSP degradation genes. Overall, our findings provide novel insights into the distribution and abundance of DMSP degradation genes in a coastal region with different water current systems.

Paraconexibacter algicola gen. nov., sp. nov., a novel actinobacterium isolated from a eutrophic lake during the end of cyanobacterial harmful algal blooms, and proposal of Paraconexibacteraceae fam. nov. in the order Solirubrobacterales.

A novel bacterium, strain Seoho-28T, was isolated from a shallow eutrophic lake during the end of cyanobacterial harmful algal blooms and was characterized taxonomically and phylogenetically. Strain Seoho-28T was a Gram-stain-negative, aerobic, rod-shaped and non-motile bacterium. The strain grew optimally with 0 % NaCl and at 25-30 °C on Reasoner's 2A medium. The phylogenetic analysis based on 16S rRNA gene sequences positioned the novel strain among the order Solirubrobacterales, but sequence similarities to known species were less than 94.7 %. The genomic DNA G+C content of the strain Seoho-28T was 74.2 mol%. Genomic comparisons of strain Seoho-28T with families in the order Solirubrobacterales were made using the Genome-to-Genome Distance Calculator, average nucleotide identity and average amino acid identity analyses (values indicated ≤14.9, ≤73.5 and ≤57.8 %, respectively). Strain Seoho-28T contained C16 : 0-iso, C18 : 1 ω9c and C16 : 0 as major fatty acids and MK-7 (H4) as the major quinone. Strain Seoho-28T contained diphosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid as major polar lipids. Meso- and ll-diaminopimelic acids were the diagnostic diamino acids in the cell-wall peptidoglycan. Based on the genotypic, chemotaxonomic and phenotypic results, strain Seoho-28T represents a novel genus and species, Paraconexibacter algicola gen. nov., sp. nov., which belongs to a new family Paraconexibacteraceae in the order Solirubrobacterales and the class Thermoleophilia. The type strain is Seoho-28T (=KCTC 39791T=JCM 31881T).

Nevskia lacus sp. nov., a gammaproteobacterium isolated from a eutrophic lake.

A novel Gram-stain negative, rod-shaped and motile bacterial strain, designated strain Seoho-38T, was isolated from a eutrophic lake in South Korea. Polyphasic taxonomic studies were performed to investigate the taxonomic position of the new isolate. The phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain Seoho-38T formed a distinct cluster with Nevskia ramosa Soe1T, Nevskia persephonica G6M-30T, Nevskia soli GR15-1T, Nevskia terrae KIS13-15T and Nevskia aquatilis F2-63T with bootstrap resampling value of 100%. Of those Nevskia strains, the new isolate shows high sequence similarity with N. ramosa Soe1T (98.7%) and N. persephonica G6M-30T (97.2%), and values lower than 96.5% with the other type strains. The new isolate was observed to grow aerobically in 0-1.5% (w/v) NaCl (optimum 0%), at pH 7.0-9.0 (optimum pH 7.0) and temperature 15-36 °C (optimum 20-30 °C) on R2A medium. DNA-DNA relatedness values between strain Seoho-38T and the type strains of reference species in the genus Nevskia were < 24%. The genomic DNA G + C content was determined to be 67.4 mol%. Ubiquinone-8 (Q-8) (95%) and ubiquinone-7 (Q-7) (5%) were identified as the respiratory quinones. The cellular polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phosphoaminolipid, two glycolipids, an aminolipid and four unidentified lipids. The major fatty acid components were found to include summed feature 3 (C16:1ω7c and/or C16:1ω6c), summed feature 8 (C18:0ω7c and/or C18:0ω6c), C16:0 and C14:0. Based on the above polyphasic evidence, strain Seoho-38T (= KCTC 52221T = JCM 31888T) represents a new species of the genus Nevskia, for which the name Nevskia lacus sp. nov. is proposed.

Ammonia oxidizers in the sea-surface microlayer of a coastal marine inlet.

Planktonic archaea are thought to play an important role in ammonia oxidation in marine environments. Data on the distribution, abundance, and diversity of ammonia oxidizers in the coastal sea-surface microlayer (SML) are lacking, despite previous reports of high abundance of Thaumarchaeota in the SML of estuaries and freshwater lakes. Here, we failed to detect the presence of ammonia-oxidizing bacteria in any of our samples taken from a semi-enclosed marine inlet in Japan. Therefore, we shifted our focus to examine the archaeal community composition as well as the Thaumarchaeota marine group I (MG-I) and ammonia monooxygenase subunit A (amoA) gene copy numbers and composition in the SML and corresponding underlying water (UW, 20 cm). amoA gene copy numbers obtained by quantitative PCR were consistent with the typical values observed in the surface waters of oceanic and coastal environments where nitrification activity has been detected, but the copy numbers were two- to three-fold less than those reported from the surface layers and UW of high mountain lakes. Both amoA and MG-I 16S rRNA gene copy numbers were significantly negatively correlated with chlorophyll-a and transparent exopolymer particle concentrations in the SML. Communities of archaea and ammonia-oxidizing archaea in SML samples collected during low wind conditions (≤5 m s-1) differed the most from those in UW samples, whereas the communities in SML samples collected during high wind conditions were similar to the UW communities. In the SML, low ratios of amoA to MG-I 16S rRNA genes were observed, implying that most of the SML Thaumarchaeota lacked amoA. To our knowledge, our results provide the first comparison of ammonia-oxidizing communities in the coastal SML with those in the UW.

Amylibacter kogurei sp. nov., a novel marine alphaproteobacterium isolated from the coastal sea surface microlayer of a marine inlet.

A novel Gram-negative bacterium, designated 4G11T, was isolated from the sea surface microlayer of a marine inlet. On the basis of 16S rRNA gene sequence analysis, the strain showed the closest similarity to Amylibacter ulvae KCTC 32465T (99.0 %). However, DNA-DNA hybridization values showed low DNA relatedness between strain 4G11T and its close phylogenetic neighbours, Amylibacter marinus NBRC 110140T (8.0±0.4 %) and Amylibacter ulvae KCTC 32465T (52.9±0.9 %). Strain 4G11T had C18 : 1, C16 : 0 and C18 : 2 as the major fatty acids. The only isoprenoid quinone detected for strain 4G11T was ubiquinone-10. The major polar lipids were phosphatidylglycerol, phosphatidylcholine, one unidentified polar lipid, one unidentified phospholipid and one unidentified aminolipid. The DNA G+C content of strain 4G11T was 50.0 mol%. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the novel strain should be assigned to a novel species, for which the name Amylibacter kogurei sp. nov. is proposed. The type strain of Amylibacter kogurei is 4G11T (KY463497=KCTC 52506T=NBRC 112428T).

Draft Genome Sequence of Saccharospirillum sp. Strain MSK14-1, Isolated from Surface Seawater Collected at Aburatsubo Inlet in Japan.

Here, we report the draft genome sequence of Saccharospirillum sp. strain MSK14-1, isolated from surface seawater collected at Aburatsubo Inlet in Japan. The genome sequence of strain MSK14-1 should contribute to our understanding of the characteristics of the genus Saccharospirillum.

Draft Genome Sequence of Rubricoccus marinus SG-29T, a Marine Bacterium within the Family Rhodothermaceae, Which Contains Two Different Rhodopsin Genes.

Here, we report the draft genome sequence of Rubricoccus marinus SG-29T, a bacterium isolated from the western North Pacific Ocean. R. marinus SG-29T possesses two different types of rhodopsin genes and belongs to the family Rhodothermaceae, with which halophilic, thermophilic, and marine bacteria are associated.

Algibacter aquaticus sp. nov., a slightly alkaliphilic marine Flavobacterium isolated from coastal surface water.

A rod-shaped, pale yellow-pigmented, aerobic, Gram-staining-negative strain with gliding motility, designated as strain SK-16T, was isolated from the coastal surface water of a semi-enclosed coastal inlet in Misaki, Japan. Analysis of 16S rRNA gene sequences revealed that SK-16T represented a member of the family Flavobacteriaceae and was closely related to the genus Algibacter, with sequence similarities ranging from 95.9 to 94.3 % to the type strains of species of the genus Algibacter. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 G and iso-C15 : 0 3-OH. Major polar lipids were phosphatidylethanolamine, an aminophospholipid and an unidentified phospholipid. The DNA G+C content of SK-16T was 32.3 mol% and MK-6 was the only predominant isoprenoid quinone. On the basis of the results of phenotypic, genotypic, chemotaxonomic and phylogenetic studies, it was suggested that SK-16T represents a novel species within the genus Algibacter, with the newly proposed name Algibacteraquaticus. The type strain is SK-16T (=NBRC 110220T=KCTC 32974T).

Draft Genome Sequences of Two Fabibacter sp. Strains Isolated from Coastal Surface Water of Aburatsubo Inlet, Japan.

Here, we report the draft genome sequences of Fabibacter sp. strain 4D4 and F. misakiensis strain SK-8T, isolated from surface seawater of a semienclosed inlet.

Draft Genome Sequence of Lewinella sp. Strain 4G2 Isolated from the Coastal Sea Surface Microlayer.

We report here the draft genome of Lewinella sp. strain 4G2, isolated from the sea surface microlayer (SML) of a coastal marine inlet. The genome sequence of strain 4G2 should contribute to understanding the lifestyles of bacteria living in the SML.

Fabibacter misakiensis sp. nov., a marine bacterium isolated from coastal surface water.

A slightly curved-rod-shaped, pink-pigmented, Gram-stain-negative, aerobic bacterial strain with gliding motility, designated SK-8T, was isolated from coastal surface water of Misaki, Japan. Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain SK-8T belonged to the genus Fabibacter and showed 96.0 % sequence similarity to the type strain of the most closely related species, Fabibacter pacificus DY53T. The novel isolate was phenotypically and physiologically different from previously described strains. The major cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. Major polar lipids were phosphatidylethanolamine, two aminophospholipids and an unidentified phospholipid. The DNA G+C content was 39.1 mol% and MK-7 was the only predominant isoprenoid quinone. On the basis of this taxonomic study employing a polyphasic approach, it was suggested that strain SK-8T represents a novel species of the genus Fabibacter, with the newly proposed name Fabibacter misakiensis sp. nov. The type strain is SK-8T ( = NBRC 110216T = KCTC 32969T).

Abundance and distribution of dimethylsulfoniopropionate degradation genes and the corresponding bacterial community structure at dimethyl sulfide hot spots in the tropical and subtropical pacific ocean.

Dimethylsulfoniopropionate (DMSP) is mainly produced by marine phytoplankton but is released into the microbial food web and degraded by marine bacteria to dimethyl sulfide (DMS) and other products. To reveal the abundance and distribution of bacterial DMSP degradation genes and the corresponding bacterial communities in relation to DMS and DMSP concentrations in seawater, we collected surface seawater samples from DMS hot spot sites during a cruise across the Pacific Ocean. We analyzed the genes encoding DMSP lyase (dddP) and DMSP demethylase (dmdA), which are responsible for the transformation of DMSP to DMS and DMSP assimilation, respectively. The averaged abundance (±standard deviation) of these DMSP degradation genes relative to that of the 16S rRNA genes was 33% ± 12%. The abundances of these genes showed large spatial variations. dddP genes showed more variation in abundances than dmdA genes. Multidimensional analysis based on the abundances of DMSP degradation genes and environmental factors revealed that the distribution pattern of these genes was influenced by chlorophyll a concentrations and temperatures. dddP genes, dmdA subclade C/2 genes, and dmdA subclade D genes exhibited significant correlations with the marine Roseobacter clade, SAR11 subgroup Ib, and SAR11 subgroup Ia, respectively. SAR11 subgroups Ia and Ib, which possessed dmdA genes, were suggested to be the main potential DMSP consumers. The Roseobacter clade members possessing dddP genes in oligotrophic subtropical regions were possible DMS producers. These results suggest that DMSP degradation genes are abundant and widely distributed in the surface seawater and that the marine bacteria possessing these genes influence the degradation of DMSP and regulate the emissions of DMS in subtropical gyres of the Pacific Ocean.