Methanotrophic Communities and Cultivation of Methanotrophs from Rice Paddy Fields Fertilized with Pig-livestock Biogas Digestive Effluent and Synthetic Fertilizer in the Vietnamese Mekong Delta.

Biogas digestive effluent (BDE) has been applied to rice fields in the Vietnamese Mekong Delta (VMD). However, limited information is available on the community composition and isolation of methanotrophs in these fields. Therefore, the present study aimed (i) to clarify the responses of the methanotrophic community in paddy fields fertilized with BDE or synthetic fertilizer (SF) and (ii) to isolate methanotrophs from these fields.

sp. nov., a heavy-metal-tolerant bacterium isolated from garden soil.

A previously undescribed, heavy-metal-tolerant, motile, Gram-negative bacterium, designated strain SK50-23, was characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SK50-23 was closely related to LMG 26467 and the non-phototrophic '' NS23 (98.1 and 97.

Detection and isolation of a new member of Burkholderiaceae-related endofungal bacteria from Saksenaea boninensis sp. nov., a new thermotolerant fungus in Mucorales.

Thermotolerance in Mucorales (Mucoromycotina) is one of the factors to be opportunistic pathogens, causing mucormycosis. Among thermotolerant mucoralean fungi, Burkholderiaceae-related endobacteria (BRE) are rarely found and the known range of hosts is limited to Rhizopus spp. The phylogenetic divergence of BRE has recently expanded in other fungal groups such as Mortierellaceae spp.

Complete genome sequence of Pseudoalteromonas sp. PS1M3, a psychrotrophic bacterium isolated from deep-sea sediment off the Boso Peninsula, Japan Trench.

Herein, we report the complete genome sequence of Pseudoalteromonas sp. PS1M3 (= NCBI 87791), which is a psychrotrophic bacterium that inhabits in seabed off the Boso Peninsula, Japan Trench. Analysis of the genomic sequence revealed that PS1M3 possesses 2 circular chromosomal DNAs and 2 circular plasmid DNAs.

A Nitrate-Transforming Bacterial Community Dominates in the Rhizosphere on Nitrogen-Deficient Volcanic Deposits of Miyake-jima.

The perennial gramineous grass functions as a major pioneer plant in colonizing acidic volcanic deposits on Miyake-jima, Japan, despite a lack of nitrogen nutrients. The nitrogen cycle in the rhizosphere is important for the vigorous growth of in this unfavorable environment. In the present study, we identified the nitrogen-cycling bacterial community in the rhizosphere on these volcanic deposits using a combination of metagenomics and culture-based analyses.

Investigating Endobacteria that Thrive Within Mucoromycota.

Metagenomics approaches have revealed the importance of Mucoromycota in the evolution and functioning of plant microbiomes. Comprised of three subphyla (Glomeromycotina, Mortierellomycotina, and Mucoromycotina), this early diverging lineage of fungi encompasses species of mycorrhizal fungi, root endophytes, plant pathogens, and many decomposers of plant debris. Interestingly, several taxa of Mucoromycota share a common feature, that is, the presence of endobacteria within their mycelia and spores.

Mitigation of Paddy Field Soil Methane Emissions by Betaproteobacterium Azoarcus Inoculation of Rice Seeds.

Paddy fields are a major source of atmospheric methane, a greenhouse gas produced by methanogens and consumed by methanotrophs in flooded soil. The inoculation of rice seeds with the bacterium Azoarcus sp. KH32C alters the rice root-associated soil bacterial community composition.

Complete Genome Sequence of a Psychrophilic Bacterium, sp. Strain APM04, Isolated from the Seafloor of the South Mariana Trough, Pacific Ocean.

The complete genome sequence of sp. strain APM04, which is a psychrophilic bacterium that inhabits the seabed of the South Mariana Trough, Pacific Ocean, was determined to characterize the genetic features associated with evolution in extremophilic and oligotrophic deep seawater.

Whole-Genome Sequence of Entomortierella parvispora E1425, a Mucoromycotan Fungus Associated with -Related Endosymbiotic Bacteria.

Some mucoromycotan fungi establish symbiotic associations with endohyphal bacteria. Here, the genome of Entomortierella parvispora E1425 (synonymously known as Mortierella parvispora E1425), which harbors a cultured -related endobacterium (BRE) designated sp. strain B2-EB, was sequenced.

Complete Genome Sequence of a Chemolithoautotrophic Iron-Oxidizing Bacterium, Acidithiobacillus ferrooxidans Strain NFP31, Isolated from Volcanic Ash Deposits on Miyake-Jima, Japan.

The genome sequence of Acidithiobacillus ferrooxidans strain NFP31, which is a chemolithoautotrophic iron-oxidizing bacterium that inhabits acidified volcanic deposits on Mount Oyama, Miyake Island (Miyake-jima), Japan, was determined to identify the genetic characteristics associated with pioneer microbes in newly placed pyroclastic deposits.

sp. Strain B2-EB: Comparative Genomics Reveals Minimal Genomic Features Required by a Cultivable -Related Endofungal Bacterium.

Obligate bacterial endosymbionts are critical to the existence of many eukaryotes. Such endobacteria are usually characterized by reduced genomes and metabolic dependence on the host, which may cause difficulty in isolating them in pure cultures. Family -related endofungal bacteria affiliated with the clade can be associated with the fungal subphyla Mortierellomycotina and Glomeromycotina.

Aposymbiosis of a Burkholderiaceae-Related Endobacterium Impacts on Sexual Reproduction of Its Fungal Host.

Bacterial endosymbionts inhabit diverse fungal lineages. Although the number of studies on bacteria is increasing, the mechanisms by which bacteria affect their fungal hosts remain unclear. We herein examined the homothallic isolate, Mortierella sugadairana YTM39, harboring a Burkholderiaceae-related endobacterium, which did not produce sexual spores.

Genome Sequence of sp. UKPF54, a Plant Growth-Promoting Rhizobacterial Strain with NO-Mitigating Abilities, Isolated from Paddy Soil.

sp. strain UKPF54, a plant growth-promoting rhizobacterium with the ability to mitigate nitrous oxide emission from agriculture soils, has been successfully isolated from paddy soil in Kumamoto, Japan. Here, we report the whole-genome sequence of this strain.

Genome Sequence of Arthrobacter sp. UKPF54-2, a Plant Growth-Promoting Rhizobacterial Strain Isolated from Paddy Soil.

sp. strain UKPF54-2, a plant growth-promoting rhizobacterium having the potential ability to control fungal and bacterial pathogens, was isolated from paddy soil in Kumamoto, Japan. We report here the whole-genome sequence of this strain.

Genome Sequences of Two Azospirillum sp. Strains, TSA2S and TSH100, Plant Growth-Promoting Rhizobacteria with NO Mitigation Abilities.

sp. strains TSA2S and TSH100 are plant growth-promoting rhizobacteria with the capacity to mitigate NO from agricultural soil. They were isolated from the rhizosphere of paddy soil in Tokyo, Japan.

Comparative Characterization of Bacterial Communities in Moss-Covered and Unvegetated Volcanic Deposits of Mount Merapi, Indonesia.

Microbial colonization, followed by succession, on newly exposed volcanic substrates represents the beginning of the development of an early ecosystem. During early succession, colonization by mosses or plants significantly alters the pioneer microbial community composition through the photosynthetic carbon input. To provide further insights into this process, we investigated the three-year-old volcanic deposits of Mount Merapi, Indonesia.

Complete Genome Sequence of a Microcystin-Degrading Bacterium, Sphingosinicella microcystinivorans Strain B-9.

Sphingosinicella microcystinivorans strain B-9 has the ability to degrade cyanobacterial hepatotoxic cyclic peptides, microcystins, and nodularins. This is the first report of the complete genome sequence of the microcystin-degrading bacterium.

Prevalence and Intra-Family Phylogenetic Divergence of Burkholderiaceae-Related Endobacteria Associated with Species of Mortierella.

Endofungal bacteria are widespread within the phylum Mucoromycota, and these include Burkholderiaceae-related endobacteria (BRE). However, the prevalence of BRE in Mortierellomycotinan fungi and their phylogenetic divergence remain unclear. Therefore, we examined the prevalence of BRE in diverse species of Mortierella.

Comparative Analysis of the Genetic Basis of Branched Nonylphenol Degradation by Sphingobium amiense DSM 16289 and Sphingobium cloacae JCM 10874.

Branched nonylphenol (BNP), a degradation product of nonylphenol polyethoxylates, exerts estrogenic effects on various organisms. The genes underlying BNP degradation by Sphingobium amiense DSM 16289 were analyzed by complete genome sequencing and compared with those of the versatile BNP-degrading Sphingobium cloacae JCM 10874. An opdA homolog (opdA) encoding BNP degradation activity was identified in DSM 16289, in contrast with JCM 10874, possessing both the opdA homolog and nmoA.

Presence of Cu-Type (NirK) and cd-Type (NirS) Nitrite Reductase Genes in the Denitrifying Bacterium Bradyrhizobium nitroreducens sp. nov.

Nitrite reductase is a key enzyme for denitrification. There are two types of nitrite reductases: copper-containing NirK and cytochrome cd-containing NirS. Most denitrifiers possess either nirK or nirS, although a few strains been reported to possess both genes.

Complete genome sequence of Agrobacterium pusense VsBac-Y9, a bacterial symbiont of the dark septate endophytic fungus Veronaeopsis simplex Y34 with potential for improving fungal colonization in roots.

A Rhizobium-related bacterium (Rhizobium sp. VsBac-Y9) is a symbiont living with the dark septate endophytic (DSE) fungus Veronaeopsis simplex Y34. Co-inoculation of Rhizobium sp.

Comparative Genomic Insights into Endofungal Lifestyles of Two Bacterial Endosymbionts, Mycoavidus cysteinexigens and Burkholderia rhizoxinica.

Endohyphal bacteria (EHB), dwelling within fungal hyphae, markedly affect the growth and metabolic potential of their hosts. To date, two EHB belonging to the family Burkholderiaceae have been isolated and characterized as new taxa, Burkholderia rhizoxinica (HKI 454) and Mycoavidus cysteinexigens (B1-EB), in Japan. Metagenome sequencing was recently reported for Mortierella elongata AG77 together with its endosymbiont M.

Effects of Rhizobium Species Living with the Dark Septate Endophytic Fungus Veronaeopsis simplex on Organic Substrate Utilization by the Host.

Bacteria harbored in/on the hyphae of the dark septate endophyte, Veronaeopsis simplex Y34, were identified as a single Rhizobium species by molecular analyses of bacterial 16S rRNA genes, and were successfully isolated from the endophyte. The Rhizobium-cured fungus was prepared thoroughly by an antibiotic treatment, thereby allowing an examination of their effects on organic substrate utilization. Assays with Biolog FF microplates revealed that the respiration potential for 52.

Complete Genome Sequence of the Nonheterocystous Cyanobacterium sp. ABRG5-3.

We report here the complete sequences of the main genome (4.8 Mb) and seven plasmids of the semifilamentous, nonheterocystous cyanobacterium sp. ABRG5-3, a strain isolated from a pond in Japan.