Oceaniferula marina gen.nov., sp.nov., an anti-fluoroquinolone bacterium isolated from marine sediment

A Gram-stain-negative, aerobic, rod-shaped, non-gliding and non-motile bacterium designated as N1E253^T, was isolated from marine sediments collected from the coast of Weihai, PR China. N1E253^T was found to grow at pH 7.0-9.0 (optimum, pH 7.5), 15-37 °C (optimum, 30 °C) in the presence of 1.5-5.0% (w/v) NaCl (optimum, 3.0%). The major polar lipids of strain N1E253^T were phosphatidylethanolamine, diphosphatidylglycerol and one unidentified phospholipid. The sole respiratory quinone was MK-9. The major cellular fatty acids (> 10.0%) were iso-C_{14: 0}, C_{16: 0} and Summed Feature 3 (C_16:1 ω7c and/or C_16:1 ω6c). The result of the 16S rRNA gene sequence analysis confirmed the affiliation of this novel isolate to the family Verrucomicrobiaceae, with Persicirhabdus sediminis KCTC 22039 ^T being its closest relative with 92.1% sequence similarity. Genome sequencing revealed a genome size of 5,073,947 bp, DNA G + C content of 52.0% and two protein-coding genes related to the resistance of fluoroquinolones. Based on physiological, genomic, biochemical and chemotaxonomic characteristics, we propose that strain N1E253^T represents a novel species of a novel genus within the family Verrucomicrobiaceae, for which the name Oceaniferula marina gen. nov., sp. nov. is proposed. The type strain is N1E253^T (= KCTC 72800 ^T = MCCC 1H00405^T).

Phragmitibacter flavus gen. nov., sp. nov. a new member of the family Verrucomicrobiaceae

The Gram-stain-negative, aerobic, non-motile, oxidase- and catalase-positive, rod-shaped yellow-coloured bacterial strain MG-N-17T was isolated from a water sample of Lake Fertő/Neusiedler See (Hungary). Results of phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain forms a distinct linage within the family Verrucomicrobiaceae of the phylum Verrucomicrobia , and its closest relatives are Verrucomicrobium spinosum DSM 4136T (94.38 %) and Roseimicrobium gellanilyticum DC2a-G7T (91.55 %). The novel bacterial strain prefers a weak alkaline environment and grows optimally between 22–28 °C in the absence of NaCl. The major isoprenoid quinones are MK-10, MK-11, MK-12 and MK-9. The major cellular fatty acids are anteiso-C15 : 0, C16 : 0, C16 : 1ω5c and iso-C14 : 0. The polar lipid profile contains phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and four unidentified glycolipids. The assembled draft genome of strain MG-N-17T had 44 contigs with an N50 value 348255 nt, 56.5× genome coverage, total length of 5 910 933 bp and G+C content of 56.9 mol%. Strain MG-N-17T (=DSM 106674T=NCAIM B.02643T) is proposed as the type strain of a new genus and species in the family Verrucomicrobiaceae , for which the name Phragmitibacter flavus gen. nov., sp. nov. is proposed.

Evolution of microbial community during dry storage and recovery of aerobic granular sludge

Aerobic granular sludge (AGS) was imbedded in agar and stored at 4 °C for 30 days, and then the stored granules were recovered in a sequencing batch reactor fed real wastewater within 11 days. Variations in microbial community compositions were investigated during dry storage and recovery of AGS, aiming to elucidate the mechanism of granular stability loss and recovery. The storage and recovery of AGS involved microbial community evolution. The dominant bacterial genera of the mature AGS were Zoogloea (relative abundance of 22.39%), Thauera (16.03%) and Clostridium_sensu_stricto (11.17%), and those of the stored granules were Acidovorax (26.79%), Macellibacteroides (12.83%) and Pseudoxanthomonas (5.69%), respectively. However, the dominant genera were Streptococcus (43.64%), Clostridium_sensu_stricto (12.3.6%) and Lactococcus (11.47%) in the recovered AGS. Methanogens were always the dominant archaeal species in mature AGS (93.01%), stored granules (99.99%) and the recovered AGS (94.84%). Facultative anaerobes and anaerobes proliferated and dominated in the stored granules, and their metabolic activities gradually led to granular structure destruction and property deterioration. However, the stored granules served as carriers for the microbes originated from the real septic tank wastewater during recovery. They proliferated rapidly and secreted a large number of extracellular polymeric substances which helped to recover the granular structure in 11 days.

The plethora of membrane respiratory chains in the phyla of life

The diversity of microbial cells is reflected in differences in cell size and shape, motility, mechanisms of cell division, pathogenicity or adaptation to different environmental niches. All these variations are achieved by the distinct metabolic strategies adopted by the organisms. The respiratory chains are integral parts of those strategies especially because they perform the most or, at least, most efficient energy conservation in the cell. Respiratory chains are composed of several membrane proteins, which perform a stepwise oxidation of metabolites toward the reduction of terminal electron acceptors. Many of these membrane proteins use the energy released from the oxidoreduction reaction they catalyze to translocate charges across the membrane and thus contribute to the establishment of the membrane potential, i.e. they conserve energy. In this work we illustrate and discuss the composition of the respiratory chains of different taxonomic clades, based on bioinformatic analyses and on biochemical data available in the literature. We explore the diversity of the respiratory chains of Animals, Plants, Fungi and Protists kingdoms as well as of Prokaryotes, including Bacteria and Archaea. The prokaryotic phyla studied in this work are Gammaproteobacteria, Betaproteobacteria, Epsilonproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Chlamydiae, Verrucomicrobia, Acidobacteria, Planctomycetes, Cyanobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Aquificae, Thermotogae, Deferribacteres, Nitrospirae, Euryarchaeota, Crenarchaeota and Thaumarchaeota.

Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS)

The growth rate is a fundamental characteristic of bacterial species, determining its contributions to the microbial community and carbon flow. High-throughput sequencing can reveal bacterial diversity, but its quantitative inaccuracy precludes estimation of abundances and growth rates from the read numbers. Here, we overcame this limitation by normalizing Illumina-derived amplicon reads using an internal standard: a constant amount of Escherichia coli cells added to samples just before biomass collection. This approach made it possible to reconstruct growth curves for 319 individual OTUs during the grazer-removal experiment conducted in a freshwater reservoir Římov. The high resolution data signalize significant functional heterogeneity inside the commonly investigated bacterial groups. For instance, many Actinobacterial phylotypes, a group considered to harbor slow-growing defense specialists, grew rapidly upon grazers' removal, demonstrating their considerable importance in carbon flow through food webs, while most Verrucomicrobial phylotypes were particle associated. Such differences indicate distinct life strategies and roles in food webs of specific bacterial phylotypes and groups. The impact of grazers on the specific growth rate distributions supports the hypothesis that bacterivory reduces competition and allows existence of diverse bacterial communities. It suggests that the community changes were driven mainly by abundant, fast, or moderately growing, and not by rare fast growing, phylotypes. We believe amplicon read normalization using internal standard (ARNIS) can shed new light on in situ growth dynamics of both abundant and rare bacteria.

Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes

Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, and yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions and greatly expand knowledge of the genomic diversity of freshwater Verrucomicrobia. Genome analysis revealed their potential role as (poly)saccharide degraders in freshwater, uncovered interesting genomic features for this lifestyle, and suggested their adaptation to nutrient availabilities in their environments. Verrucomicrobia populations differ significantly between the two lakes in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially derived allochthonous carbon sources of the two ecosystems, respectively. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochrome c complex and might be involved in extracellular electron transfer in the anoxic humus-rich environment. Notably, most epilimnion genomes have large numbers of so-called "Planctomycete-specific" cytochrome c-encoding genes, which exhibited distribution patterns nearly opposite to those seen with glycoside hydrolase genes, probably associated with the different levels of environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes represent a major step toward understanding the role, ecophysiology, and distribution of Verrucomicrobia in freshwater. IMPORTANCE Freshwater Verrucomicrobia spp. are cosmopolitan in lakes and rivers, and yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia spp. are restricted to one subdivision of this phylum. Here, we greatly expanded the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent the first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia to be potential (poly)saccharide degraders and suggested their adaptation to carbon sources of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called "Planctomycete-specific" cytochrome c-encoding genes and identified their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology, and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling.

Terrimicrobium sacchariphilum gen. nov., sp. nov., an anaerobic bacterium of the class ‘Spartobacteria’ in the phylum Verrucomicrobia, isolated from a rice paddy field

A strictly anaerobic, mesophilic, carbohydrate-fermenting bacterium, designated NM-5T, was isolated from a rice paddy field. Cells of strain NM-5T were Gram-stain-negative, non-motile, non-spore-forming, short rods (0.5–0.7 µm×0.6–1.2 µm). The strain grew optimally at 37 °C (growth range 20–40 °C) and pH 7.0 (pH 5.5–8.0). The strain could grow fermentatively on arabinose, xylose, fructose, galactose, glucose, ribose, mannose, cellobiose, lactose, maltose and sucrose. The main end-products of glucose fermentation were acetate and propionate. Organic acids, alcohols and amino acids were not utilized for growth. Yeast extract was not required but stimulated the growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite, and Fe (III) nitrilotriacetate were not used as terminal electron acceptors. The DNA G+C content was 46.3 mol%. The major cellular fatty acids were iso-C14 : 0, C18 : 0 and C16 : 0. 16S rRNA gene sequence analysis revealed that strain NM-5T belongs to the class ‘S partobacteria’, subdivision 2 of the bacterial phylum Verrucomicrobia . Phylogenetically, the closest species was ‘Chthoniobacter flavus’ (89.6 % similarity in 16S rRNA gene sequence). A novel genus and species, Terrimicrobium sacchariphilum gen. nov., sp. nov., is proposed. The type strain of the type species is NM-5T ( = JCM 17479T = CGMCC 1.5168T).