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PubMed2006

A molecular phylogenetic analysis of the Octocorallia (Cnidaria: Anthozoa) based on mitochondrial protein-coding sequences.

Despite their abundance and ecological importance in a wide variety of shallow and deep water marine communities, octocorals (soft corals, sea fans, and sea pens) are a group whose taxonomy and phylogenetic relationships remain poorly known and little studied. The group is currently divided into three orders (O: Alcyonacea, Pennatulacea, and Helioporacea); the large O. Alcyonacea (soft corals and sea fans) is further subdivided into six sub-ordinal groups on the basis of skeletal composition and colony growth form. We used 1429bp of two mitochondrial protein-coding genes, ND2 and msh1, to construct a phylogeny for 103 octocoral genera representing 28 families. In agreement with a previous 18S rDNA phylogeny, our results support a division of Octocorallia into two major clades plus a third, minor clade. We found one large clade (Holaxonia-Alcyoniina) comprising the sea fan sub-order Holaxonia and the majority of soft corals, and a second clade (Calcaxonia-Pennatulacea) comprising sea pens (O. Pennatulacea) and the sea fan sub-order Calcaxonia. Taxa belonging to the sea fan group Scleraxonia and the soft coral family Alcyoniidae were divided among the Holaxonia-Alcyoniina clade and a third, small clade (Anthomastus-Corallium) whose relationship to the two major clades was unresolved. In contrast to the previous studies, we found sea pens to be monophyletic but nested within Calcaxonia; our analyses support the sea fan family Ellisellidae as the sister taxon to the sea pens. We are unable to reject the hypothesis that the calcaxonian and holaxonian skeletal axes each arose once and suggest that the skeletal axis of sea pens is derived from that of Calcaxonia. Topology tests rejected the monophyly of sub-ordinal groups Alcyoniina, Scleraxonia, and Stolonifera, as well as 9 of 14 families for which we sampled multiple genera. The much broader taxon sampling and better phylogenetic resolution afforded by our study relative to the previous efforts greatly clarify the relationships among families and sub-ordinal groups within each of the major clades. The failure of these mitochondrial genes as well as previous 18S rDNA studies to resolve many of the deeper nodes within the tree (including its root) suggest that octocorals underwent a rapid radiation and that large amounts of sequence data will be required in order to resolve the basal relationships within the clade.

Animals↗
PubMed1993

Sequential differentiation of sensory innervation in the mystacial pad of the ferret.

The mystacial pad of the ferret has an elaborate sensory innervation provided by three types of terminal nerves that arise from the infraorbital branch of the trigeminal nerve. Deep and superficial vibrissal nerves innervate nearly exclusive targets in the large follicle-sinus complexes (F-SCs) at the base of each tactile vibrissa. Dermal plexus nerves innervate the fur between the vibrissae. Each type of nerve provides a similar variety of sensory endings, albeit to different targets. In this study, Winkelmann and Sevier-Munger reduced silver techniques revealed that most of the endings differentiate postnatally in an overlapping sequence like that observed previously in the rat. Afferents from the deep vibrissal nerves begin to differentiate first, followed successively by those from superficial vibrissal nerves and the dermal plexus. Within each type of nerve, Merkel endings begin to differentiate first, followed successively by lanceolate endings and circumferential endings. In the ferret, the differentiation of the intervibrissal fur and its innervation is slightly delayed but substantially overlaps the development of the vibrissal innervation, whereas in the rat it occurs almost entirely later. There was no evidence of a transient exuberant or misplaced innervation or other secondary remodeling. Differentiating afferents and endings are located only in the sites normally seen in the adult, suggesting a high degree of afferent-target specificity. In the ferret, innervation is virtually lacking in one target--the inner conical body of the F-SCs, which is densely innervated in the rat. This lack was due to a failure of innervation to develop rather than to a secondary elimination of a transient innervation.

Animals↗
PubMed2003

Natural selection for polymorphism in the disease resistance gene Rps2 of Arabidopsis thaliana.

Pathogen resistance is an ecologically important phenotype increasingly well understood at the molecular genetic level. In this article, we examine levels of avrRpt2-dependent resistance and Rps2 locus DNA sequence variability in a worldwide sample of 27 accessions of Arabidopsis thaliana. The rooted parsimony tree of Rps2 sequences drawn from a diverse set of ecotypes includes a deep bifurcation separating major resistance and susceptibility clades of alleles. We find evidence for selection maintaining these alleles and identify the N-terminal part of the leucine-rich repeat region as a probable target of selection. Additional protein variants are found within the two major clades and correlate well with measurable differences among ecotypes in resistance to the avirulence gene avrRpt2 of the pathogen Pseudomonas syringae. Long-lived polymorphisms have been observed for other resistance genes of A. thaliana; the Rps2 data suggest that the long-term maintenance of phenotypic variation in resistance genes may be a general phenomenon and are consistent with diversifying selection acting in concert with selection to maintain variation.

Arabidopsis↗
PubMed2006

Molecular analysis of the nitrogen cycle in deep-sea microorganisms from the Nankai Trough: genes for nitrification and denitrification from deep-sea environmental DNA.

Nitrification and denitrification are bacterial functions, which are important for the global nitrogen cycle. Thus, it is important to study the diversity and distribution of bacteria in the environment, which are involved in the nitrogen cycle on the earth. Ammonia monooxygenase encoded by the amoA gene and nitrite reductase encoded by nirK or nirS are essential enzymes for nitrificaton and denitrification, respectively. These genes can be used as markers for the identification of organisms in the nitrogen cycle. In this study, we identified amoA (42 clones) and nirS (98 clones) genes in parallel from samples recovered from the deep-sea of the Nankai Trough. Genes for nirK could not be amplified from these samples. The obtained amoA sequences were not so closely related to those of amoA genes from previously isolated environmental organisms and those of genes from environmental DNAs. On the other hand, the nirS genes sequenced showed some relationship to some extent with the latter genes. However, some of the newly sequenced genes formed clusters, which contained no previously identified genes on a phylogenetic tree. These are likely present in specific denitrifiers from the deep-sea. The results of this study further suggest that nitrifiers and denitrifiers live in the same area of the Nankai Trough and the nitrogen cycle exists even in the deep-sea.

DNA↗
PubMed2003

An index of substitution saturation and its application.

We introduce a new index to measure substitution saturation in a set of aligned nucleotide sequences. The index is based on the notion of entropy in information theory. We derive the critical values of the index based on computer simulation with different sequence lengths, different number of OTUs and different topologies. The critical value enables researchers to quickly judge whether a set of aligned sequences is useful in phylogenetics. We illustrate the index by applying it to an analysis of the aligned sequences of the elongation factor-1alpha gene originally used to resolve the deep phylogeny of major arthropod groups. The method has been implemented in DAMBE.

Base Sequence↗
PubMed2005

Genotyping of Candida albicans on the basis of polymorphisms of ALT repeats in the repetitive sequence (RPS).

BACKGROUND: Candida albicans is one of the most important etiologic agents causing superficial and deep fungal infections. For prevention of candidiasis, it is important to develop a rapid system that discriminates C. albicans at the strain level. OBJECTIVE: To develop a system that can identify C. albicans at the strain level. METHODS: Genomic DNAs were purified from 179 clinical isolates of C. albicans, and were used as templates for PCR amplification of 25S rDNA and ALT repeats in repetitive sequences (RPSs). PCR products generated from ALT repeats were digested with EcoRI and/or ClaI in order to study the relationships between restriction profiles and amplification profiles. RESULTS: One hundred and seventy nine clinical isolates were grouped into genotypes A (92 isolates), B (38 isolates) and C (49 isolates) on the basis of their 25S rDNA, and each was further classified into five types (types 3, 4, 3/4, 2/3/4 and 3/4/5) by PCR amplification targeting ALT repeats. Type 3 C. albicans constituted the majority of isolates in any genotypes (66.3% for genotype A, 76.3% for genotype B and 73.4% for genotype C). Each C. albicans type showed several amplification patterns, indicating the existence of subtypes. RFLP analysis revealed that restriction profiles of PCR products corresponded to amplification patterns from PCR. CONCLUSION: The present results indicate that PCR amplifications targeting 25S rDNA and ALT repeats are useful for rapid genotyping and distinction of C. albicans involved in superficial candidiasis.

Candida albicans↗
PubMed2006

In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India.

BACKGROUND: Macrohaplogroups 'M' and 'N' have evolved almost in parallel from a founder haplogroup L3. Macrohaplogroup N in India has already been defined in previous studies and recently the macrohaplogroup M among the Indian populations has been characterized. In this study, we attempted to reconstruct and re-evaluate the phylogeny of Macrohaplogroup M, which harbors more than 60% of the Indian mtDNA lineage, and to shed light on the origin of its deep rooting haplogroups. RESULTS: Using 11 whole mtDNA and 2231 partial coding sequence of Indian M lineage selected from 8670 HVS1 sequences across India, we have reconstructed the tree including Andamanese-specific lineage M31 and calculated the time depth of all the nodes. We defined one novel haplogroup M41, and revised the classification of haplogroups M3, M18, and M31. CONCLUSION: Our result indicates that the Indian mtDNA pool consists of several deep rooting lineages of macrohaplogroup 'M' suggesting in-situ origin of these haplogroups in South Asia, most likely in the India. These deep rooting lineages are not language specific and spread over all the language groups in India. Moreover, our reanalysis of the Andamanese-specific lineage M31 suggests population specific two clear-cut subclades (M31a1 and M31a2). Onge and Jarwa share M31a1 branch while M31a2 clade is present in only Great Andamanese individuals. Overall our study supported the one wave, rapid dispersal theory of modern humans along the Asian coast.

DNA, Mitochondrial↗
PubMed1984

The development of axonal connections in the central olfactory system of rats.

The development of the cytoarchitecture and axonal connections of the central olfactory system were studied in fetal and neonatal rats from E16. In contrast to neocortical development, the olfactory cortex lacks a distinct cortical plate. In the piriform cortex and the olfactory tubercle the cellular laminae emerge simultaneously, while in the anterior olfactory nucleus, there are morphogenetic gradients from superficial to deep as well as from caudal to rostral which parallel the known cytogenetic gradients. Parallel morphogenetic and cytogenetic gradients are also present in the lateral to medial axis of the olfactory tubercle. The projection from the olfactory bulb and the associational projections from the piriform cortex begin to develop well before birth. At E17 fibers from the bulb are limited to the lateral olfactory tract (LOT) and the molecular layer just deep to it, and then spread out caudally, laterally, and medially away from the LOT. This sequence of innervation parallels and predicts the density of innervation in the adult: those areas which are innervated first (such as the piriform cortex deep to the LOT) ultimately receive the heaviest innervation; conversely, those areas which are innervated very late (such as the medial olfactory tubercle) receive the lightest projection. The intracortical projections from the anterior and posterior piriform cortex extend into layer I ipsilaterally by E20 and obtain their adult distribution by the middle of the first postnatal week. On the other hand, fibers from the anterior olfactory nucleus and the entorhinal area do not reach their full adult extent until the second postnatal week. Similarly, the crossed projection of the anterior piriform cortex to the contralateral posterior piriform cortex does not grow into layer I until this later time. The timing of fiber ingrowth showed no relation to the trajectory or eventual areal or laminar termination of fibers. As with the olfactory bulb projection, the timing may influence the density of termination. Centrifugal fibers to the bulb are demonstrable around the time of birth both by the retrograde transport of horseradish peroxidase (HRP) and by the anterograde transport of 3H-leucine. The arrival of additional fibers during the remainder of the first postnatal week parallels the known cytogenetic and morphogenetic gradients in the areas in which they arise. The projections of the olfactory cortex to the lateral hypothalamic area and the mediodorsal thalamic nucleus are evident before birth. This correlates with the early generation of the cells which give rise to these projections.

Aging↗
PubMed2000

Dynamics and phylogenetic implications of MtDNA control region sequences in New World Jays (Aves: Corvidae).

To study the evolution of mtDNA and the intergeneric relationships of New World Jays (Aves: Corvidae), we sequenced the entire mitochondrial DNA control region (CR) from 21 species representing all genera of New World jays, an Old World jay, crows, and a magpie. Using maximum likelihood methods, we found that both the transition/transversion ratio (kappa) and among site rate variation (alpha) were higher in flanking domains I and II than in the conserved central domain and that the frequency of indels was highest in domain II. Estimates of kappa and alpha were much more influenced by the density of taxon sampling than by alternative optimal tree topologies. We implemented a successive approximation method incorporating these parameters into phylogenetic analysis. In addition we compared our study in detail to a previous study using cytochrome b and morphology to examine the effect of taxon sampling, evolutionary rates of genes, and combined data on tree resolution. We found that the particular weighting scheme used had no effect on tree topology and little effect on tree robustness. Taxon sampling had a significant effect on tree robustness but little effect on the topology of the best tree. The CR data set differed nonsignificantly from the tree derived from the cytochrome b/morphological data set primarily in the placement of the genus Gymnorhinus, which is near the base of the CR tree. However, contrary to conventional taxonomy, the CR data set suggested that blue and black jays (Cyanocorax sensu lato) might be paraphyletic and that the brown jay Psilorhinus (=Cyanocorax) morio is the sister group to magpie jays (Calocitta), a phylogenetic hypothesis that is likely as parsimonious with regard to nonmolecular characters as monophyly of Cyanocorax. The CR tree also suggests that the common ancestor of NWJs was likely a cooperative breeder. Consistent with recent systematic theory, our data suggest that DNA sequences with high substitution rates such as the CR may nonetheless be useful in reconstructing relatively deep phylogenetic nodes in avian groups.

Animals↗
PubMed1998

Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms

Because excised, washed roots of rice (Oryza sativa) immediately produce CH4 when they are incubated under anoxic conditions (P. Frenzel and U. Bosse, FEMS Microbiol. Ecol. 21:25-36, 1996), we employed a culture-independent molecular approach to identify the methanogenic microbial community present on roots of rice plants. Archaeal small-subunit rRNA-encoding genes were amplified directly from total root DNA by PCR and then cloned. Thirty-two archaeal rice root (ARR) gene clones were randomly selected, and the amplified primary structures of ca. 750 nucleotide sequence positions were compared. Only 10 of the environmental sequences were affiliated with known methanogens; 5 were affiliated with Methanosarcina spp., and 5 were affiliated with Methanobacterium spp. The remaining 22 ARR gene clones formed four distinct lineages (rice clusters I through IV) which were not closely related to any known cultured member of the Archaea. Rice clusters I and II formed distinct clades within the phylogenetic radiation of the orders "Methanosarcinales" and Methanomicrobiales. Rice cluster I was novel, and rice cluster II was closely affiliated with environmental sequences obtained from bog peat in northern England. Rice cluster III occurred on the same branch as Thermoplasma acidophilum and marine group II but was only distantly related to these taxa. Rice cluster IV was a deep-branching crenarchaeotal assemblage that was closely related to clone pGrfC26, an environmental sequence recovered from a temperate marsh environment. The use of a domain-specific oligonucleotide probe in a fluorescent in situ hybridization analysis revealed that viable members of the Archaea were present on the surfaces of rice roots. In addition, we describe a novel euryarchaeotal main line of descent, designated rice cluster V, which was detected in anoxic rice paddy soil. These results indicate that there is an astonishing richness of archaeal diversity present on rice roots and in the surrounding paddy soil.

Journal Article↗
PubMed2026

Metagenome-based vertical profiling of the Gulf of Mexico highlights its uniqueness and far-reaching effects of freshwater input.

Genomic and metagenomic explorations of the oceans have identified well-structured microbial assemblages showing endemic genomic adaptations with increasing depth. However, deep water column surveys have been limited, especially of the Gulf of Mexico (GoM) basin, despite its importance for human activities. To fill this gap, we report on 19 deeply sequenced (~5 Gbp/sample) shotgun metagenomes collected along a vertical gradient, from the surface to about 2,000 m deep, at three GoM stations. Beta diversity analysis revealed strong clustering by depth, and not by station. However, a community-level pangenome style gene content analysis revealed ~54% of predicted gene sequences to be station-specific within our GoM samples. Of the 154 medium-to-high-quality MAGs recovered, 145 represent novel species compared with the NCBI genomes and Tara Oceans MAGs databases. Two of these MAGs were relatively abundant at both surface and deep samples, revealing remarkable versatility across the water column. A few MAGs of freshwater origin (~6% of total detected) were relatively abundant at 600 m deep and 270 miles from the coast at one station, revealing that the effects of freshwater input in the GoM can sometimes be far-reaching and long-lasting. Notably, 1,447/16,068 of the total COGs detected were positively (Pearson's r ≥ 0.5) or negatively (Pearson's r ≤ -0.5) correlated with depth, including beta-lactamases, dehydrogenases, and CoA-associated oxidoreductases. Taken together, our results reveal substantial novel genome and gene diversity across the GoM's water column, and testable hypotheses for some of the diversity patterns observed.IMPORTANCETo what extent microbial communities are similar between different ocean basins at similar depths, and what the impact of freshwater input by major rivers may be on these communities, remain poorly understood issues with potentially important implications for modeling and managing marine biodiversity. In this study, we performed metagenomic sequencing and recovered 154 medium-to-high-quality metagenome-assembled genomes (MAGs) from three stations in the Gulf of Mexico (GoM) and from various depths up to about 2,000 m. Comparison to MAGs recovered from other ocean basins highlighted the unique diversity harbored by the GoM, which could be driven by more substantial input from the Mississippi River and by human activities, including offshore oil drilling. The data and results provided by this study should be useful for future comparative analysis of marine biodiversity and contribute to its more complete characterization.

Metagenome↗
PubMed2004

The GC-rich transposon Bytmar1 from the deep-sea hydrothermal crab, Bythograea thermydron, may encode three transposase isoforms from a single ORF.

Mariner-like elements (MLEs) are classII transposons with highly conserved sequence properties and are widespread in the genome of animal species living in continental environments. We describe here the first full-length MLE found in the genome of a marine crustacean species, the deep-sea hydrothermal crab Bythograea thermydron (Crustacea), named Bytmar1. A comparison of its sequence features with those of the MLEs contained in the genomes of continental species reveals several distinctive characteristics. First, Bytmar1 elements contains an ORF that may encode three transposase isoforms 349, 379, and 398 amino acids (aa) in long. The two biggest proteins are due to the presence of a 30- and 49-aa flag, respectively, at the N-terminal end of the 349-aa cardinal MLE transposase. Their GC contents are also significantly higher than those found in continental MLEs. This feature is mainly due to codon usage in the transposase ORF and directly interferes with the curvature propensities of the Bytmar1 nucleic acid sequence. Such an elevated GC content may interfere with the ability of Bytmar 1 to form an excision complex and, in consequence, with its efficiency to transpose. Finally, the origin of these characteristics and their possible consequences on transposition efficiency are discussed.

Amino Acid Sequence↗
PubMed2026

IQ-NET: fast and accurate quartet phylogenetic inference using deep learning trained on empirical DNA alignments.

Phylogenetic inference is fundamental to modern biology, with many applications including evolutionary biology, epidemiology, and comparative genomics. While maximum likelihood and Bayesian methods remain the gold standard for phylogenetic analysis, they rely on simplifying assumptions and are computationally intensive. Recent machine learning approaches for phylogenetics offer speed advantages, but have several limitations: exclusive reliance on simulated data for training, inadequate handling of gaps, and sensitivity to input sequence order. Here, we introduce IQ-NET (Intelligent Quartet NETwork), a deep learning framework that solves these limitations to infer four-taxon trees. IQ-NET estimates both tree topology and branch lengths directly from gapped alignments. IQ-NET outperforms existing machine learning methods in terms of accuracy, and obtained a 24-fold speedup compared with the widely used maximum likelihood software, IQ-TREE. We finally introduce a pipeline using IQ-NET and the ASTRAL software to reconstruct a larger species tree, i.e., with more than four taxa.

Empirical data training↗
PubMed1997

Germ-layer surface tensions and "tissue affinities" in Rana pipiens gastrulae: quantitative measurements.

The morphogenetic properties causing germ-layer spreading and stratification in amphibian gastrulation were called "tissue affinities" by Holtfreter. The differential adhesion hypothesis (DAH) attributes such liquid-like tissue rearrangements to forces generated by intercellular adhesions within and between the migrating cell populations. This theory predicts that, among the primary germ layers, the cohesiveness of deep ectoderm should be the greatest, that of deep mesoderm should be intermediate, and that of deep endoderm should be the least. Also, the cohesiveness of differentiating neural ectoderm should increase after induction, causing it to internalize and segregate from epidermis. The DAH also explains why the cohesiveness of "liquid" tissues, whose cells are free to rearrange, should be measurable as tissue surface tensions. Using a specially designed tissue surface tensiometer, we demonstrate that (i) aggregates of Rana pipiens deep germ layers do possess liquid-like surface tensions, (ii) their surface tension values lie in precisely the sequence necessary to account for germ-layer stratification in vitro and in vivo, and (iii) the surface tension of deep ectoderm just underlain by the archenteron roof is twice that of not-yet-underlain deep ectoderm. These measurements provide direct, quantitative evidence that the "tissue affinities" governing germ-layer flow during early stages of vertebrate morphogenesis are reflected in tissue surface tensions.

Animals↗
PubMed1998

A deep brain photoreceptive molecule in the toad hypothalamus.

We have isolated a cDNA clone encoding a deep brain photoreceptive molecule from the hypothalamic cDNA library of the toad, Bufo japonicus. The deduced amino acid sequence showed the highest similarity to that of pinopsin (75-76%) among vertebrate retinal opsins, indicating the expression of toad pinopsin in the deep brain. Antibodies raised against the C-terminal tail of toad pinopsin stained cell bodies and the knob-like structures of the cerebrospinal fluid-contacting neurons in the anterior preoptic nucleus. This region is known to play an important role in breeding behavior, suggesting that toad pinopsin acts as a photosensor for the photoperiodic gonadal response.

Amino Acid Sequence↗
PubMed2024

A deep learning framework for denoising and ordering scRNA-seq data using adversarial autoencoder with dynamic batching.

Single-cell RNA sequencing (scRNA-seq) provides high resolution of cell-to-cell variation in gene expression and offers insights into cell heterogeneity, differentiating dynamics, and disease mechanisms. However, technical challenges such as low capture rates and dropout events can introduce noise in data analysis. Here, we present a deep learning framework, called the dynamic batching adversarial autoencoder (DB-AAE), for denoising scRNA-seq datasets. First, we describe steps to set up the computing environment, training, and tuning. Then, we depict the visualization of the denoising results. For complete details on the use and execution of this protocol, please refer to Ko et al.1.

Deep Learning↗
PubMed1996

Fluid-attenuated inversion recovery (FLAIR) for assessment of cerebral infarction. Initial clinical experience in 50 patients.

BACKGROUND AND PURPOSE: Our aim was to evaluate fluid-attenuated inversion recovery (FLAIR) sequence in the diagnosis of cerebral infarction with MRI. METHODS: A retrospective review was undertaken of 50 consecutive MRI studies ordered for suspected cerebrovascular accident. All studies included FLAIR and rapid acquisition with relaxation enhancement (RARE) T2-weighted spin-echo sequences. The two sequences were compared independently by four observers at two different institutions. Detectability of lesions and image quality were scored. RESULTS: Overall, FLAIR sequences proved superior in 10 patients, detecting acute cortical infarcts missed with RARE spin-echo technique in five patients. In five additional patients, improved characterization of chronic infarction and improved detection of microangiopathic deep hemispheric changes were observed. One brain stem infarct was missed with the FLAIR sequence. CONCLUSIONS: FLAIR offers advantages in detection of acute infarcts affecting the cortical ribbon, is a useful, rapid adjunct to conventional T2-weighted spin-echo sequences, and has the potential to replace these in the future.

Artifacts↗
PubMed2003

Isolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolithoautotrophic alpha- and gamma-proteobacteria from the deep sea.

We report the isolation and physiological characterization of novel, psychrophilic, iron-oxidizing bacteria (FeOB) from low-temperature weathering habitats in the vicinity of the Juan de Fuca deep-sea hydrothermal area. The FeOB were cultured from the surfaces of weathered rock and metalliferous sediments. They are capable of growth on a variety of natural and synthetic solid rock and mineral substrates, such as pyrite (FeS(2)), basalt glass ( approximately 10 wt% FeO), and siderite (FeCO(3)), as their sole energy source, as well as numerous aqueous Fe substrates. Growth temperature characteristics correspond to the in situ environmental conditions of sample origin; the FeOB grow optimally at 3 to 10 degrees C and at generation times ranging from 57 to 74 h. They are obligate chemolithoautotrophs and grow optimally under microaerobic conditions in the presence of an oxygen gradient or anaerobically in the presence of nitrate. None of the strains are capable of using any organic or alternate inorganic substrates tested. The bacteria are phylogenetically diverse and have no close Fe-oxidizing or autotrophic relatives represented in pure culture. One group of isolates are gamma-Proteobacteria most closely related to the heterotrophic bacterium Marinobacter aquaeolei (87 to 94% sequence similarity). A second group of isolates are alpha-Proteobacteria most closely related to the deep-sea heterotrophic bacterium Hyphomonas jannaschiana (81 to 89% sequence similarity). This study provides further evidence for the evolutionarily widespread capacity for Fe oxidation among bacteria and suggests that FeOB may play an unrecognized geomicrobiological role in rock weathering in the deep sea.

Alphaproteobacteria↗