The metagenomics of biosilicification: causes and effects

AbstractIn order to determine the links between geochemical parameters controlling the formation of silica sinter in hot springs and their associated microbial diversity, a detailed characterisation of the waters and ofin situ-grown silica sinters was combined with molecular phylogenetic analyses of the bacterial communities in Icelandic geothermal environments. At all but one site, the microorganisms clearly affected, and in part controlled, the formation of the macroscopic textures and structures of silica sinter edifices. In addition, the class and genera level phylogenetic diversity and distribution appeared to be closely linked to variations in temperature, salinity and pH regimes.

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Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

Applied and Environmental Microbiology ◽

10.1128/aem.00294-14 ◽

2014 ◽

Vol 80 (12) ◽

pp. 3677-3686 ◽

Cited By ~ 100

Author(s):

Jun Liu ◽

Zheng-Shuang Hua ◽

Lin-Xing Chen ◽

Jia-Liang Kuang ◽

Sheng-Jin Li ◽

...

Keyword(s):

Microbial Diversity ◽

Community Composition ◽

Environmental Conditions ◽

Mine Tailings ◽

Large Scale ◽

Hot Springs ◽

Mine Drainage ◽

Rrna Gene ◽

Content Type ◽

Geochemical Parameters

ABSTRACTRecent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within theAlphaproteobacteria,Deltaproteobacteria, andFirmicuteswere attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.

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Molecular Phylogenetic Diversity and Spatial Distribution of Bacterial Communities in Cooling Stage during Swine Manure Composting

Asian-Australasian Journal of Animal Sciences ◽

10.5713/ajas.14.0882 ◽

2015 ◽

Vol 28 (6) ◽

pp. 888-895 ◽

Cited By ~ 7

Author(s):

Yan Guo ◽

Jinliang Zhang ◽

Yongfeng Yan ◽

Jian Wu ◽

Nengwu Zhu ◽

...

Keyword(s):

Spatial Distribution ◽

Bacterial Communities ◽

Phylogenetic Diversity ◽

Swine Manure ◽

Cooling Stage ◽

Molecular Phylogenetic

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Infection Dynamics of Coexisting Beta- and Gammaproteobacteria in the Nested Endosymbiotic System of Mealybugs

Applied and Environmental Microbiology ◽

10.1128/aem.00250-08 ◽

2008 ◽

Vol 74 (13) ◽

pp. 4175-4184 ◽

Cited By ~ 66

Author(s):

Marie Kono ◽

Ryuichi Koga ◽

Masakazu Shimada ◽

Takema Fukatsu

Keyword(s):

Population Dynamics ◽

Phylogenetic Analyses ◽

Reproductive Activity ◽

Adult Males ◽

Female Development ◽

Male Development ◽

Infection Dynamics ◽

Molecular Phylogenetic ◽

Pseudococcus Comstocki

ABSTRACT We investigated the infection dynamics of endosymbiotic bacteria in the developmental course of the mealybugs Planococcus kraunhiae and Pseudococcus comstocki. Molecular phylogenetic analyses identified a betaproteobacterium and a gammaproteobacterium from each of the mealybug species. The former bacterium was related to the β-endosymbionts of other mealybugs, i.e., “Candidatus Tremblaya princeps,” and formed a compact clade in the Betaproteobacteria. Meanwhile, the latter bacterium was related to the γ-endosymbionts of other mealybugs but belonged to distinct clades in the Gammaproteobacteria. Whole-mount in situ hybridization confirmed the peculiar nested formation in the endosymbiotic system of the mealybugs: the β-endosymbiont cells were present in the cytoplasm of the bacteriocytes, and the γ-endosymbiont cells were located in the β-endosymbiont cells. In nymphal and female development, a large oval bacteriome consisting of a number of bacteriocytes was present in the abdomen, wherein the endosymbionts were harbored. In male development, strikingly, the bacteriome progressively degenerated in prepupae and pupae and became almost unrecognizable in adult males. In the degeneration process, the γ-endosymbionts disappeared more rapidly than the β-endosymbionts did. Quantitative PCR analyses revealed that (i) the population dynamics of the endosymbionts in female development reflected the reproductive activity of the insects, (ii) the population dynamics of the endosymbionts were strikingly different between female development and male development, (iii) the endosymbiont populations drastically decreased in male development, and (iv) the γ-endosymbiont populations decreased more rapidly than the β-endosymbiont populations in male development. Possible mechanisms underlying the uncoupled regulation of the β- and γ-endosymbiont populations are discussed in relation to the establishment and evolution of this unique prokaryote-prokaryote endosymbiotic system.

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Tripartite organization of the ancestral chordate brain and the antiquity of placodes: insights from ascidian Pax-2/5/8, Hox and Otx genes

Development ◽

10.1242/dev.125.6.1113 ◽

1998 ◽

Vol 125 (6) ◽

pp. 1113-1122 ◽

Cited By ~ 13

Author(s):

H. Wada ◽

H. Saiga ◽

N. Satoh ◽

P.W. Holland

Keyword(s):

Neural Tube ◽

Hox Genes ◽

Phylogenetic Analyses ◽

Nervous Systems ◽

Vertebrate Brain ◽

Molecular Phylogenetic ◽

Central Nervous Systems ◽

Single Precursor ◽

In Situ Hybridizations

Ascidians and vertebrates belong to the Phylum Chordata and both have dorsal tubular central nervous systems. The structure of the ascidian neural tube is extremely simple, containing less than 400 cells, among which less than 100 cells are neurons. Recent studies suggest that, despite its simple organization, the mechanisms patterning the ascidian neural tube are similar to those of the more complex vertebrate brain. Identification of homologous regions between vertebrate and ascidian nervous systems, however, remains to be resolved. Here we report the expression of HrPax-258 gene: an ascidian homologue of vertebrate Pax-2, Pax-5 and Pax-8 genes. Molecular phylogenetic analyses indicate that HrPax-258 is descendant from a single precursor gene that gave rise to the three vertebrate genes. The expression pattern of HrPax-258 suggests that this subfamily of Pax genes has conserved roles in regional specification of the brain. Comparison with expression of ascidian Otx (Hroth) and a Hox gene (HrHox1) by double-staining in situ hybridizations indicate that the ascidian brain region can be subdivided into three regions; the anterior region marked by Hroth probably homologous to the vertebrate forebrain and midbrain, the middle region marked by HrPax-258 probably homologous to the vertebrate anterior hindbrain (and maybe also midbrain) and the posterior region marked by Hox genes which is homologous to the vertebrate hindbrain and spinal cord. Later expression of HrPax-258 in atrial primordia implies that basal chordates such as ascidians have already acquired a sensory organ that develops from epidermal thickenings (placodes) and expresses HrPax-258; we suggest it is homologous to the vertebrate ear. Therefore, placodes are not likely to be a newly acquired feature in vertebrates, but may have already been possessed by the earliest chordates.

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Aerobic Biodegradation of Methyltert-Butyl Ether by Aquifer Bacteria from Leaking Underground Storage Tank Sites

Applied and Environmental Microbiology ◽

10.1128/aem.67.12.5824-5829.2001 ◽

2001 ◽

Vol 67 (12) ◽

pp. 5824-5829 ◽

Cited By ~ 57

Author(s):

S. R. Kane ◽

H. R. Beller ◽

T. C. Legler ◽

C. J. Koester ◽

H. C. Pinkart ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Butyl Alcohol ◽

Water Soluble ◽

Aerobic Biodegradation ◽

Butyl Ether ◽

Degrading Bacterium ◽

In Situ Conditions ◽

Molecular Phylogenetic ◽

Mtbe Degradation

ABSTRACT The potential for aerobic methyl tert-butyl ether (MTBE) degradation was investigated with microcosms containing aquifer sediment and groundwater from four MTBE-contaminated sites characterized by oxygen-limited in situ conditions. MTBE depletion was observed for sediments from two sites (e.g., 4.5 mg/liter degraded in 15 days after a 4-day lag period), whereas no consumption of MTBE was observed for sediments from the other sites after 75 days. For sediments in which MTBE was consumed, 43 to 54% of added [U-14C]MTBE was mineralized to14CO2. Molecular phylogenetic analyses of these sediments indicated the enrichment of species closely related to a known MTBE-degrading bacterium, strain PM1. At only one site, the presence of water-soluble gasoline components significantly inhibited MTBE degradation and led to a more pronounced accumulation of the metabolite tert-butyl alcohol. Overall, these results suggest that the effects of oxygen and water-soluble gasoline components on in situ MTBE degradation will vary from site to site and that phylogenetic analysis may be a promising predictor of MTBE biodegradation potential.

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Two Intracellular Symbiotic Bacteria from the Mulberry Psyllid Anomoneura mori (Insecta, Homoptera)

Applied and Environmental Microbiology ◽

10.1128/aem.64.10.3599-3606.1998 ◽

1998 ◽

Vol 64 (10) ◽

pp. 3599-3606 ◽

Cited By ~ 134

Author(s):

Takema Fukatsu ◽

Naruo Nikoh

Keyword(s):

In Situ Hybridization ◽

16S Rdna ◽

Phylogenetic Analyses ◽

Symbiotic Bacteria ◽

Polymorphism Analysis ◽

16S Rdna Sequence ◽

Rdna Sequences ◽

16S Rdna Sequences ◽

Molecular Phylogenetic

ABSTRACT We characterized the intracellular symbiotic bacteria of the mulberry psyllid Anomoneura mori by performing a molecular phylogenetic analysis combined with in situ hybridization. In its abdomen, the psyllid has a large, yellow, bilobed mycetome (or bacteriome) which consists of many round uninucleated mycetocytes (or bacteriocytes) enclosing syncytial tissue. The mycetocytes and syncytium harbor specific intracellular bacteria, the X-symbionts and Y-symbionts, respectively. Almost the entire length of the bacterial 16S ribosomal DNA (rDNA) was amplified and cloned from the whole DNA ofA. mori, and two clones, the A-type and B-type clones, were identified by restriction fragment length polymorphism analysis. In situ hybridization with specific oligonucleotide probes demonstrated that the A-type and B-type 16S rDNAs were derived from the X-symbionts and Y-symbionts, respectively. Molecular phylogenetic analyses of the 16S rDNA sequences showed that these symbionts belong to distinct lineages in the γ subdivision of the Proteobacteria. No 16S rDNA sequences in the databases were closely related to the 16S rDNA sequences of the X- and Y-symbionts. However, the sequences that were relatively closely related to them were the sequences of endosymbionts of other insects. The nucleotide compositions of the 16S rDNAs of the X- and Y-symbionts were highly AT biased, and the sequence of the X-symbiont was the most AT-rich bacterial 16S rDNA sequence reported so far.

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