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In this study, a novel bacterium designated F3b2T was isolated from the gut sample of weaver ant Oecophylla smaragdina and characterised. Strain F3b2T was a Gram-negative, aerobic, non-motile, ovoid-shaped bacterium and grows optimally at 28–30 °C. Its major respiratory quinone is ubiquinone 10 (Q-10) and the major fatty acids are C18:1ω7c, C19:0 cyclo ω8c and C16:0, representing 85% of the total fatty acids. The 16S rRNA gene sequence of strain F3b2T was highest in similarity to that of Oecophyllibacter saccharovorans DSM106907T and Swingsia samuieinsis NBRC 107927T at 94.35% and 91.96%, respectively. A 16S rRNA gene-based phylogenetic analysis and a core genes-based phylogenomic analysis placed strain F3b2T in a distinct lineage in the family Acetobacteraceae. The phylogenetic placement was supported by lower than species delineation threshold average nucleotide identity (ANI) (≤ 70.2%), in silico DNA-DNA hybridization (DDH) (≤ 39.5%) and average amino acid identity (AAI) (≤ 63.5%) values between strain F3b2T and closest neighbours. These overall genome relatedness indices also supported the assignment of strain F3b2T to a novel genus within Acetobacteraceae. The genome of strain F3b2T was 1.96 Mb with 60.4% G + C DNA content. Based on these results, strain F3b2T represented a novel taxon of Acetobacteraceae, for which we proposed the name Formicincola oecophyllae gen. nov. sp. nov., and strain F3b2T (= LMG 30590T = DSM 106908T = NBRC 113640T = KCTC 62951T) as the type strain. [ABSTRACT FROM AUTHOR]

Annotated genome sequences provide valuable insight into the functional capabilities of members of microbial communities. Nevertheless, most studies on the microbiome in animal guts use metagenomic data, hampering the assignment of genes to specific microbial taxa. Here, we make use of the readily culturable bacterial communities in the gut of the fruit fly Drosophila melanogaster to obtain draft genome sequences for 96 isolates from wild flies. These include 81 new de novo assembled genomes, assigned to three orders (Enterobacterales, Lactobacillales, and Rhodospirillales) with 80% of strains identified to species level using average nucleotide identity and phylogenomic reconstruction. Based on annotations by the RAST pipeline, among-isolate variation in metabolic function partitioned strongly by bacterial order, particularly by amino acid metabolism (Rhodospirillales), fermentation, and nucleotide metabolism (Lactobacillales) and arginine, urea, and polyamine metabolism (Enterobacterales). Seven bacterial species, comprising 2–3 species in each order, were well-represented among the isolates and included ≥5 strains, permitting analysis of metabolic functions in the accessory genome (i.e. genes not present in every strain). Overall, the metabolic function in the accessory genome partitioned by bacterial order. Two species, Gluconobacter cerinus (Rhodospirillales) and Lactiplantibacillus plantarum (Lactobacillales) had large accessory genomes, and metabolic functions were dominated by amino acid metabolism (G. cerinus) and carbohydrate metabolism (La. plantarum). The patterns of variation in metabolic capabilities at multiple phylogenetic scales provide the basis for future studies of the ecological and evolutionary processes shaping the diversity of microorganisms associated with natural populations of Drosophila. [ABSTRACT FROM AUTHOR]

Molecular phylogenetics and phylogenomics are subject to noise from horizontal gene transfer (HGT) and bias from convergence in macromolecular compositions. Extensive variation in size, structure and base composition of alphaproteobacterial genomes has complicated their phylogenomics, sparking controversy over the origins and closest relatives of the SAR11 strains. SAR11 are highly abundant, cosmopolitan aquatic Alphaproteobacteria with streamlined, A+T-biased genomes. A dominant view holds that SAR11 are monophyletic and related to both Rickettsiales and the ancestor of mitochondria. Other studies dispute this, finding evidence of a polyphyletic origin of SAR11 with most strains distantly related to Rickettsiales. Although careful evolutionary modeling can reduce bias and noise in phylogenomic inference, entirely different approaches may be useful to extract robust phylogenetic signals from genomes. Here we develop simple phyloclassifiers from bioinformatically derived tRNA Class-Informative Features (CIFs), features predicted to target tRNAs for specific interactions within the tRNA interaction network. Our tRNA CIF-based model robustly and accurately classifies alphaproteobacterial genomes into one of seven undisputed monophyletic orders or families, despite great variability in tRNA gene complement sizes and base compositions. Our model robustly rejects monophyly of SAR11, classifying all but one strain as Rhizobiales with strong statistical support. Yet remarkably, conventional phylogenetic analysis of tRNAs classifies all SAR11 strains identically as Rickettsiales. We attribute this discrepancy to convergence of SAR11 and Rickettsiales tRNA base compositions. Thus, tRNA CIFs appear more robust to compositional convergence than tRNA sequences generally. Our results suggest that tRNA-CIF-based phyloclassification is robust to HGT of components of the tRNA interaction network, such as aminoacyl-tRNA synthetases. We explain why tRNAs are especially advantageous for prediction of traits governing macromolecular interactions from genomic data, and why such traits may be advantageous in the search for robust signals to address difficult problems in classification and phylogeny.

Members of the alphaproteobacterial order Rhodobacterales are metabolically diverse and highly abundant in the ocean. They are becoming increasingly interesting for marine biotechnology, due to their ecological adaptability, wealth of versatile low-copy-number plasmids, and their ability to produce secondary metabolites. However, molecular tools for engineering strains of this bacterial lineage are limited. Here, we expand the genetic toolbox by establishing standardized, modular repABC -based plasmid vectors of four well-characterized compatibility groups from the Roseobacter group applicable in the Rhodobacterales, and likely in further alphaproteobacterial orders (Hyphomicrobiales, Rhodospirillales, Caulobacterales). We confirmed replication of these newly constructed pABC vectors in two members of Rhodobacterales, namely, Dinoroseobacter shibae DFL 12 and Rhodobacter capsulatus B10S, as well as in two members of the alphaproteobacterial order Hyphomicrobiales (synonym: Rhizobiales; Ensifer meliloti 2011 and " Agrobacterium fabrum " C58). Maintenance of the pABC vectors in the biotechnologically valuable orders Rhodobacterales and Hyphomicrobiales facilitates the shuttling of genetic constructs between alphaproteobacterial genera and orders. Additionally, plasmid replication was verified in one member of Rhodospirillales ( Rhodospirillum rubrum S1) as well as in one member of Caulobacterales ( Caulobacter vibrioides CB15N). The modular construction of pABC vectors and the usage of four compatible replication systems, which allows their coexistence in a host cell, are advantageous features for future implementations of newly designed synthetic pathways. The vector applicability was demonstrated by functional complementation of a nitrogenase mutant phenotype by two complementary pABC-based plasmids in R. capsulatus .

The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.

A Gram-stain-negative, catalase-positive and oxidase-positive, nonmotile, aerobic, light yellow, spherical-shaped bacterial strain with no flagella, designated strain YIM 152171 T , was isolated from sediment of the South China Sea. Colonies were smooth and convex, light yellow and circular, and 1.0-1.5×1.0-1.5 µm in cell diameter after 7 days of incubation at 28°C on YIM38 media supplemented with sea salt. Colonies could grow at 20-45°C (optimum 28-35°C) and pH 6.0-11.0 (optimum, pH 7.0-9.0), and they could proliferate in the salinity range of 0-6.0 % (w/v) NaCl. The major cellular fatty acids were summed feature 8 (C 18 : 1  ω 7 c /C 18 : 1  ω6 c ), C 18 : 1  ω7 c 11-methyl, C 16 : 0 , C 16 : 1  ω11 c , C 16 : 1  ω5 c , C 17 : 1  ω6 c and C 18 : 1  ω5 c . The respiratory quinone was ubiquinone 10, and the polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol mannoside, one unidentified phospholipid and one unidentified aminolipid. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain YIM 152171 T within the order Rhodospirillales in a distinct lineage that also included the genus Geminicoccus . The 16S rRNA gene sequence similarities of YIM 152171 T to those of Arboricoccus pini , Geminicoccus roseus and Constrictibacter antarcticus were 92.17, 89.25 and 88.91 %, respectively. The assembled draft genome of strain YIM 152171 T had 136 contigs with an N50 value of 134704 nt, a total length of 3 001 346 bp and a G+C content of 70.27 mol%. The phylogenetic, phenotypic and chemotaxonomic data showed that strain YIM 152171 T (=MCCC 1K08488 T =KCTC 92884 T ) represents a type of novel species and genus for which we propose the name Marinimicrococcus gen. nov., sp. nov.

A highly settleable microalga, Ettlia sp., was applied to a freshwater recirculating aquaculture system (RAS) of Danio rerio to improve the treatment of nitrogenous compounds. The growth characteristics of the microalgae, water quality parameters, and bacterial communities were monitored for 73 days. In the treatment RAS, the inoculated Ettlia sp. grew up to 1.26 g/L and dominated (>99%) throughout the experiment, whereas naturally occurring microalgae grew to 0.57 g/L in the control RAS. The nitrate, nitrite, and ammonium concentrations in the treatment RAS were reduced by 50.1%, 73.3%, and 24.2%, respectively, compared to the control RAS. A bacterial community analysis showed that Rhodospirillales , Phycisphaerae , Chlorobiales , and Burkholderiales were the major bacterial groups in the later phase of the treatment RAS. Meanwhile, a network analysis among the Ettlia sp., bacterial groups, and environmental parameters, revealed that the bacterial groups played key roles in both water quality improvement and Ettlia sp. growth. In conclusion, the inoculation and growth of the Ettlia sp. and its associated bacteria in the RAS produced beneficial effects on the water quality by reducing the nitrogenous compounds and providing a favorable environment for certain bacterial groups to further improve water quality. [ABSTRACT FROM AUTHOR]

Bacterial strain B29T1 T was isolated from the endophytic microbial community of a Pinus pinaster tree trunk and characterized. Strain B29T1 T stained Gram-negative and formed diplococci that grew optimally at 26–30 °C and at pH 6.0–7.0. The G + C content of the DNA was 61.6 mol%. The respiratory quinone was ubiquinone 10 (UK-10), and the major fatty acids were C 16:0 , cyclo-C 19:0 ω 8 c and C 18:0 12-methyl, representing 64% of the total fatty acids. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain B29T1 T within the order Rhodospirillales in a distinct lineage that also included the genus Geminicoccus . The 16S rRNA gene sequence similarities of B29T1 T to that of Candidatus Alysiomicrobium bavaricum, Geminicoccus roseus and Candidatus Alysiosphaera europeae were 92.6%, 89.9% and 89.2%, respectively. The analysis of the available genomes from the closest families showed 177 core genes that reveals a novel family-level clade including the type strain of the genus Geminicoccus and the strain B29T1 T . Analysis of B29T1 T genome revealed all the genes involved in autotrophic carbon dioxide fixation via the reductive pentose phosphate pathway and genes encoding for starch/glycogen and chitin degradation. The phylogenetic, phenotypic and chemotaxonomic data showed that strain B29T1 T (=CIP 110763 T , =LMG 27745 T ) represents the type of a novel species and genus, for which we propose the name Arboriscoccus pini gen. nov., sp. nov. A new family ( Geminicoccaceae fam. nov.) is proposed for Arboriscoccus , Geminicoccus , Candidatus Alysiomicrobium and Candidatus Alysiosphaera. The description of the Geminicoccus roseus DSM 18922 T is also emended. [ABSTRACT FROM AUTHOR]

This study investigated the variation in microbially induced concrete corrosion communities at different circumferential locations of a real sewer pipe and the effects of a wastewater flooding event on the community. Three distinct microbial community groups were found in different corrosion samples. The physico-chemical properties of the corrosion layers and the microbial communities were distinct for the cross-sectional positions within the pipe, ie ceiling, wall and tidal zones. The microbial communities detected from the same positions in the pipe were consistent over the length of the pipe, as well as being consistent between the replicate pipes. The dominating ceiling communities were members of the bacterial orders Rhodospirillales, Acidithiobacillales, Actinomycetales, Xanthomonadales and Acidobacteriales. The wall communities were composed of members of the Xanthomonadales, Hydrogenophilales, Chromatiales and Sphingobacteriales. The tidal zones were dominated by eight bacterial and one archaeal order, with the common physiological trait of anaerobic metabolism. Sewage flooding within the sewer system did not change the tidal and wall communities, although the corrosion communities in ceiling samples were notably different, becoming more similar to the wall and tidal samples. This suggests that sewage flooding has a significant impact on the corrosion community in sewers. [ABSTRACT FROM PUBLISHER]

This is the first study of the highest elevation cyanobacteria-dominated microbial mat yet described. The desiccated mat was sampled in 2010 from an ephemeral rock pool at 5500 m above sea level in the Cordillera Vilcanota of southern Perú. After being frozen for 6 years at −20 °C in the lab, pieces of the mat were sequenced to fully characterize both the 16 and 18S microbial communities and experiments were conducted to determine if organisms in the mat could revive and become active under the extreme freeze-thaw conditions that these mats experience in the field. Sequencing revealed an unexpectedly diverse, multi-trophic microbial community with 16S OTU richness comparable to similar, seasonally desiccated mats from the Dry Valleys of Antarctica and low elevation sites in the Atacama Desert region. The bacterial community of the mat was dominated by phototrophs in the Cyanobacteria ( Nostoc) and the Rhodospirillales, whereas the eukaryotic community was dominated by predators such as bdelloid rotifers (Philodinidae). Microcosm experiments showed that bdelloid rotifers in the mat were able to come out of dormancy and actively forage even under realistic field conditions (diurnal temperature fluctuations of −12 °C at night to + 27 °C during the day), and after being frozen for 6 years. Our results broaden our understanding of the diversity of life in periodically desiccated, high-elevation habitats and demonstrate that extreme freeze-thaw cycles per se are not a major factor limiting the development of at least some members of these unique microbial mat systems. [ABSTRACT FROM AUTHOR]

A spiral-shaped, highly motile bacterium was isolated from freshwater sulfidic sediment. Strain J10T is a facultative autotroph utilizing sulfide, thiosulfate, and sulfur as the electron donors in microoxic conditions. Despite high 16S rRNA gene sequence sequence identity to Magnetospirillum gryphiswaldense MSR-1 T (99.6 %), digital DNA-DNA hybridisation homology and average nucleotide identity between the two strains was of the different species level (25 % and 83 %, respectively). Strain J10T is not magnetotactic. The DNA G + C content of strain J10T is 61.9 %. The predominant phospholipid ester-linked fatty acids are C18:1ω7, C16:1ω7, and C16:0. Strain J10T (=DSM 23205 T = VKM B-3486 T) is the first strain of the genus Magnetospirillum showing lithoautotrophic growth and is proposed here as a novel species, Magnetospirillum sulfuroxidans sp. nov. In addition, we propose to establish a framework for distinguishing genera and families within the order Rhodospirillales based on phylogenomic analysis using the threshold values for average amino acid identity at ̴ 72 % for genera and ̴ 60 % for families. According to this, we propose to divide the existing genus Magnetospirillum into three genera: Magnetospirillum , Paramagnetospirillum , and Phaeospirillum , constituting a separate family Magnetospirillaceae fam. nov. in the order Rhodospirillales. Furthermore, phylogenomic data suggest that this order should accomodate six more new family level groups including Magnetospiraceae fam. nov., Magnetovibrionaceae fam. nov., Dongiaceae fam. nov., Niveispirillaceae fam. nov., Fodinicurvataceae fam. nov., and Oceanibaculaceae fam. nov. [ABSTRACT FROM AUTHOR]

Bacterial metabolisms are responsible for critical chemical transformations in nearly all environments, including oceans, freshwater, and soil. Despite the ubiquity of bacteria in the atmosphere, little is known about the metabolic functioning of atmospheric bacterial communities. To gain a better understanding of the metabolism of bacterial communities in the atmosphere, we used a combined empirical and model-based approach to investigate the structure and composition of potentially active bacterial communities in air sampled at a high elevation research station. We found that the composition of the putatively active bacterial community (assayed via rRNA) differed significantly from the total bacterial community (assayed via rDNA). Rare taxa in the total (rDNA) community were disproportionately active relative to abundant taxa, and members of the order Rhodospirillales had the highest potential for activity. We developed theory to explore the effects of random sampling from the rRNA and rDNA communities on observed differences between the communities. We found that random sampling, particularly in cases where active taxa are rare in the rDNA community, will give rise to observed differences in community composition including the occurrence of phantom taxa, taxa which are detected in the rRNA community but not the rDNA community. We show that the use of comparative rRNA/rDNA techniques can reveal the structure and composition of the metabolically active portion of bacterial communities. Our observations suggest that metabolically active bacteria exist in the atmosphere, and that these communities may be involved in the cycling of organic compounds in the atmosphere.

Shortly after the deposition of black shales in the Rhaetian Sea (Central European Basin, CEB), the Triassic/Jurassic (Tr/J) boundary witnessed one of the Big Five mass extinction events in Earth's history. Aiming at a better understanding of paleoenvironmental changes in the (geochemically) less well-known middle to late Rhaetian (German subdivision), we studied samples from a cored borehole from the central Rhaetian Sea in NW Germany (Hebelermeer 2). Biomarkers, palynomorphs and bulk geochemistry all support a marine/brackish setting with inputs from terrestrial plants. Dinosteranes were found throughout the core, most likely suggesting the spread of dinoflagellates. It is widely accepted that volcanic exhalations during the development of the Central Atlantic Magmatic Province (CAMP) had a major impact on marine and terrestrial environments in the earliest Jurassic e.g., the development of photic zone euxinia and H 2 S poisoning of benthic life. There is evidence from the studied core, however, that comparable conditions already thrived in the central Rhaetian Sea during the middle Rhaetian. A first indication of euxinia/anoxia is evident from low to very low total organic carbon versus total sulfur (TOC/TS) ratios (~<1) with a minimum preceding the Tr/J boundary (0.03). The latter very low value hints at a decoupling of S and C cycles and eventually abiogenic pyrite formation. Water-column anoxia during the middle Rhaetian is indicated by the occurrence of the biomarker gammacerane, which records ciliates living at the O 2 -H 2 S chemocline. The strongest support for a stratified water column even with photic zone euxinia comes from high abundances of isorenieratane. This biomarker is a pigment of anoxygenic phototrophic green sulfur bacteria, which use H 2 S for photosynthesis. Our data point to perturbations in the biogeochemical cycles of sulfur and carbon already in the middle Rhaetian, which are possibly linked to early volcanic activities and SO 2 , H 2 S, and CO 2 eruptions. [ABSTRACT FROM AUTHOR]

Plant growth-promoting bacteria (PGPB) represent a promising alternative to the massive use of industrial fertilizers in agriculture. Gluconacetobacter diazotrophicus is a PGPB that colonizes several plant species. Although this bacterium is able to grow at high sucrose concentrations, its response to environmental stresses is poorly understood. The present study evaluated G. diazotrophicus PAL5 response to stresses caused by sucrose, PEG 400, NaCl, KCl, Na2SO4 and K2SO. Morphological, ultrastructural and cell growth analysis revealed that G. diazotrophicus PAL5 is more sensitive to salt than osmotic stress. Growth inhibition and strong morphological changes were caused by salinity, in consequence of Cl ion-specific toxic effect. Interestingly, low osmotic stress levels were beneficial for bacterial multiplication, which was able to tolerate high sucrose concentrations, NaSO and KSO. Our data show that G. diazotrophicus PAL5 has differential response to osmotic and salinity stress, which may influence its use as inoculant in saline environments. [ABSTRACT FROM AUTHOR]

Thereaction center core (RCC) complex and the RCC with associatedFenna–Matthews–Olson protein (FMO-RCC) complex fromthe green sulfur bacterium Chlorobaculum tepidumwerestudied comparatively by steady-state and time-resolved fluorescence(TRF) and femtosecond time-resolved transient absorption (TA) spectroscopies.The energy transfer efficiency from the FMO to the RCC complex wascalculated to be ∼40% based on the steady-state fluorescence.TRF showed that most of the FMO complexes (66%), regardless of thefact that they were physically attached to the RCC, were not ableto transfer excitation energy to the reaction center. The TA spectraof the RCC complex showed a 30–38 ps lifetime component regardlessof the excitation wavelengths, which is attributed to charge separation.Excitonic equilibration was shown in TA spectra of the RCC complexwhen excited into the BChl aQxband at 590 nm and the Chl aQyband at 670 nm, while excitation at 840 nm directlypopulated the low-energy excited state and equilibration within theexcitonic BChl amanifold was not observed. The TAspectra for the FMO-RCC complex excited into the BChl aQxband could be interpreted by a combinationof the excited FMO protein and RCC complex. The FMO-RCC complex showedan additional fast kinetic component compared with the FMO proteinand the RCC complex, which may be due to FMO-to-RCC energy transfer. [ABSTRACT FROM AUTHOR]

Ferruginous Lake Matano, Indonesia hosts one of the deepest anoxygenic photosynthetic communities on Earth. This community is dominated by low-light adapted, BChl e-synthesizing green sulfur bacteria ( GSB), which comprise ~25% of the microbial community immediately below the oxic-anoxic boundary ( OAB; 115-120 m in 2010). The size of this community is dependent on the mixing regime within the lake and the depth of the OAB-at ~117 m, the GSB live near their low-light limit. Slow growth and C-fixation rates suggest that the Lake Matano GSB can be supported by sulfide even though it only accumulates to scarcely detectable (low μ m to n m) concentrations. A model laboratory strain ( Chlorobaculum tepidum) is indeed able to access HS− for oxidation at n m concentrations. Furthermore, the GSB in Lake Matano possess a full complement of S-oxidizing genes. Together, this physiological and genetic information suggests that deep-water GSB can be supported by a S-cycle, even under ferruginous conditions. The constraints we place on the metabolic capacity and physiology of GSB have important geobiological implications. Biomarkers diagnostic of GSB would be a good proxy for anoxic conditions but could not discriminate between euxinic and ferruginous states, and though GSB biomarkers could indicate a substantial GSB community, such a community may exist with very little metabolic activity. The light requirements of GSB indicate that at light levels comparable to those in the OAB of Lake Matano or the Black Sea, GSB would have contributed little to global ocean primary production, nutrient cycling, and banded iron formation (BIF) deposition in the Precambrian. Before the proliferation of oxygenic photosynthesis, shallower OABs and lower light absorption in the ocean's surface waters would have permitted greater light availability to GSB, potentially leading to a greater role for GSB in global biogeochemical cycles. [ABSTRACT FROM AUTHOR]

A strain of acidogenic bacterium was isolated from the fermentation liquid of Cantonese-style rice vinegar produced by traditional surface fermentation. 16S rDNA identification confirmed the bacterium as Gluconacetobacter xylinus, which synthesizes bacterial cellulose, and the acid productivity of the strain was investigated. In the study, the effects of the membrane integrity and the comparison of the air–liquid interface membrane with immerged membrane on total acidity, cellulose production, alcohol dehydrogenase (ADH) activity and number of bacteria were investigated. The cellulose membrane and the bacteria were observed under SEM for discussing their relationship. The correlations between oxygen consumption and total acid production rate were compared in surface and shake flask fermentation. The results showed the average acid productivity of the strain was 0.02 g/(100 mL/h), and the integrity of cellulose membrane in surface fermentation had an important effect on total acidity and cellulose production. With a higher membrane integrity, the total acidity after 144 h of fermentation was 3.75 g/100 mL, and the cellulose production was 1.71 g/100 mL after 360 h of fermentation. However, when the membrane was crushed by mechanical force, the total acidity and the cellulose production were as low as 0.36 g/100 mL and 0.14 g/100 mL, respectively. When the cellulose membrane was forced under the surface of fermentation liquid, the total acid production rate was extremely low, but the activity of ADH in the cellulose membrane was basically the same with the one above the liquid surface. The bacteria were mainly distributed in the cellulose membrane during the fermentation. The bacterial counts in surface fermentation were more than in the shake flask fermentation and G. xylinus consumed the substrate faster in surface fermentation than in shake flask fermentation. The oxygen consumption rate and total acid production rate of surface fermentation were respectively 26.13 times and 2.92 times that of shake flask fermentation. [ABSTRACT FROM PUBLISHER]

Abstract: This study evaluates the response of the bacterial communities to different mercury (Hg) amendments in temperate forest soils. Seven soils were spiked with increasing amounts of Hg [(0, 0.032, 0.32, 3.2 and 32 μg Hg(II) g−1 dry soil]. After 30 days, we examined the bioavailable Hg using bacterial biosenors (mer-lux), basal respiration, bacterial community structures and identified indicator OTUs which were responsive to Hg. In soils treated with at least 3.2 μg Hg g−1 dry soil, resulting in bioavailable Hg higher than 0.004 μg Hg g−1 dry soil, the basal respiration was strongly affected. High bioavailable Hg also caused significant changes in the bacterial T-RFLP profiles. Members of the Alphaproteobacteria (Rhodospirillales) and Betaproteobacteria (Burkholderiales) were found to be Hg-tolerant. Here, we propose a critical limit concentration for soluble Hg of 0.004 μg Hg g−1 soil. [Copyright &y& Elsevier]

Granulibacter bethesdensis is a Gram-negative pathogen in patients with chronic granulomatous disease (CGD), a deficiency in the phagocyte NADPH oxidase. Repeated isolation of genetically identical strains from the same patient over years, and prolonged waxing and waning seropositivity in some subjects, raises the possibility of long-term persistence. G. bethesdensis resists killing by serum, CGD polymorphonuclear leukocytes (PMN), and antimicrobial peptides, indicating resistance to nonoxidative killing mechanisms. Although G. bethesdensis extends the survival of PMN, persistent intracellular bacterial survival might rely on longer-lived macrophages and their precursor monocytes. Therefore, we examined phagocytic killing by primary human monocytes and monocyte-derived macrophages (MDM). Cells from both normal and CGD subjects internalized G. bethesdensis similarly. G. bethesdensis stimulated superoxide production in normal monocytes, but to a lesser degree than in normal PMN. Normal but not CGD monocytes and MDM killed G. bethesdensis and required in vitro treatment with IFN-γ to maintain this killing effect. Although in vitro IFN-γ did not enhance G. bethesdensis killing in CGD monocytes, it restricted growth in proportion to CGD PMN residual superoxide production, providing a potential method to identify patients responsive to IFN-γ therapy. In IFN-γ-treated CGD MDM, G. bethesdensis persisted for the duration of the study (7 d) without decreasing viability of the host cells. These results indicate that G. bethesdensis is highly resistant to oxygen-independent microbicides of myeloid cells, requires an intact NADPH oxidase for clearance, and can persist long-term in CGD mononuclear phagocytes, most likely relating to the persistence of this microorganism in infected CGD patients. [ABSTRACT FROM AUTHOR]

Summary A metagenomic analysis of two aquifer systems located under a dairy farming region was performed to examine to what extent the composition and function of microbial communities varies between confined and surface-influenced unconfined groundwater ecosystems. A fundamental shift in taxa was seen with an overrepresentation of Rhodospirillales, Rhodocyclales, Chlorobia and Circovirus in the unconfined aquifer, while Deltaproteobacteria and Clostridiales were overrepresented in the confined aquifer. A relative overrepresentation of metabolic processes including antibiotic resistance (β-lactamase genes), lactose and glucose utilization and DNA replication were observed in the unconfined aquifer, while flagella production, phosphate metabolism and starch uptake pathways were all overrepresented in the confined aquifer. These differences were likely driven by differences in the nutrient status and extent of exposure to contaminants of the two groundwater systems. However, when compared with freshwater, ocean, sediment and animal gut metagenomes, the unconfined and confined aquifers were taxonomically and metabolically more similar to each other than to any other environment. This suggests that intrinsic features of groundwater ecosystems, including low oxygen levels and a lack of sunlight, have provided specific niches for evolution to create unique microbial communities. Obtaining a broader understanding of the structure and function of microbial communities inhabiting different groundwater systems is particularly important given the increased need for managing groundwater reserves of potable water. [ABSTRACT FROM AUTHOR]

Harnessing chemosynthetic symbionts is a recurring evolutionary strategy. Eukaryotes from six phyla as well as one archaeon have acquired chemoautotrophic sulfur-oxidizing bacteria. In contrast to this broad host diversity, known bacterial partners apparently belong to two classes of bacteria-the Gamma- and Epsilonproteobacteria. Here, we characterize the intracellular endosymbionts of the mouthless catenulid flatworm genus Paracatenula as chemoautotrophic sulfur-oxidizing Alphaproteobacteria. The symbionts of Paracatenula galateia are provisionally classified as "Candidatus Riegeria galateiae" based on 16S ribosomal RNA sequencing confirmed by fluorescence in situ hybridization together with functional gene and sulfur metabolite evidence. 16S rRNA gene phylogenetic analysis shows that all 16 Paracatenula species examined harbor host species-specific intracellular Candidatus Riegeria bacteria that form a monophyletic group within the order Rhodospirillales. Comparing host and symbiont phylogenies reveals strict cocladogenesis and points to vertical transmission of the symbionts. Between 33% and 50% of the body volume of the various worm species is composed of bacterial symbionts, by far the highest proportion among all known endosymbiotic associations between bacteria and metazoans. This symbiosis, which likely originated more than 500 Mya during the early evolution of flatworms, is the oldest known animal-chemoautotrophic bacteria association. The distant phylogenetic position of the symbionts compared with other mutualistic or parasitic Alphaproteobacteria promises to illuminate the common genetic predispositions that have allowed several members of this class to successfully colonize eukaryote cells. [ABSTRACT FROM AUTHOR]