Single Phylum Research Articles

Biosynthetic gene clusters from uncultivated soil bacteria of the Atacama Desert.

Soil microorganisms mediate several biological processes through the secretion of natural products synthesized in specialized metabolic pathways, yet functional characterization in ecological contexts remains challenging. Using culture-independent metagenomic analyses of microbial DNA derived directly from soil samples, we examined the potential of biosynthetic gene clusters (BGCs) from six bacterial communities distributed along an altitudinal gradient of the Andes Mountains in the Atacama Desert. We mined 38 metagenome-assembled genomes (MAGs) and identified 168 BGCs. Results indicated that most predicted BGCs were classified as non-ribosomal-peptides (NRP), post-translational modified peptides (RiPP), and terpenes, which were mainly identified in genomes of species from Acidobacteriota and Proteobacteria phyla. Based on BGC composition according to types of core biosynthetic genes, six clusters of MAGs were observed, three of them with predominance for a single phylum, of which two also showed specificity to a single sampling site. Comparative analyses of accessory genes in BGCs showed associations between membrane transporters and other protein domains involved in specialized metabolism with classes of biosynthetic cores, such as resistance-nodulation-cell division (RND) multidrug efflux pumps with RiPPs and the iron-dependent transporter TonB with terpenes. Our findings increase knowledge regarding the biosynthetic potential of uncultured bacteria inhabiting pristine locations from one of the oldest and driest nonpolar deserts on Earth.IMPORTANCEMuch of what we know about specialized metabolites in the Atacama Desert, including Andean ecosystems, comes from isolated microorganisms intended for drug development and natural product discovery. To complement research on the metabolic potential of microbes in extreme environments, comparative analyses on functional annotations of biosynthetic gene clusters (BGCs) from uncultivated bacterial genomes were carried out. Results indicated that in general, BGCs encode for structurally unique metabolites and that metagenome-assembled genomes did not show an obvious relationship between the composition of their core biosynthetic potential and taxonomy or geographic distribution. Nevertheless, some members of Acidobacteriota showed a phylogenetic relationship with specific metabolic traits and a few members of Proteobacteria and Desulfobacterota exhibited niche adaptations. Our results emphasize that studying specialized metabolism in environmental samples may significantly contribute to the elucidation of structures, activities, and ecological roles of microbial molecules.

Comparative genomic analysis of Planctomycetota potential for polysaccharide degradation identifies biotechnologically relevant microbes

BackgroundMembers of the Planctomycetota phylum harbour an outstanding potential for carbohydrate degradation given the abundance and diversity of carbohydrate-active enzymes (CAZymes) encoded in their genomes. However, mainly members of the Planctomycetia class have been characterised up to now, and little is known about the degrading capacities of the other Planctomycetota. Here, we present a comprehensive comparative analysis of all available planctomycetotal genome representatives and detail encoded carbohydrolytic potential across phylogenetic groups and different habitats.ResultsOur in-depth characterisation of the available planctomycetotal genomic resources increases our knowledge of the carbohydrolytic capacities of Planctomycetota. We show that this single phylum encompasses a wide variety of the currently known CAZyme diversity assigned to glycoside hydrolase families and that many members encode a versatile enzymatic machinery towards complex carbohydrate degradation, including lignocellulose. We highlight members of the Isosphaerales, Pirellulales, Sedimentisphaerales and Tepidisphaerales orders as having the highest encoded hydrolytic potential of the Planctomycetota. Furthermore, members of a yet uncultivated group affiliated to the Phycisphaerales order could represent an interesting source of novel lytic polysaccharide monooxygenases to boost lignocellulose degradation. Surprisingly, many Planctomycetota from anaerobic digestion reactors encode CAZymes targeting algal polysaccharides – this opens new perspectives for algal biomass valorisation in biogas processes.ConclusionsOur study provides a new perspective on planctomycetotal carbohydrolytic potential, highlighting distinct phylogenetic groups which could provide a wealth of diverse, potentially novel CAZymes of industrial interest.

A standardized archaeal taxonomy for the Genome Taxonomy Database.

The accrual of genomic data from both cultured and uncultured microorganisms provides new opportunities to develop systematic taxonomies based on evolutionary relationships. Previously, we established a bacterial taxonomy through the Genome Taxonomy Database. Here, we propose a standardized archaeal taxonomy that is derived from a 122-concatenated-protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence. The resulting archaeal taxonomy, which forms part of the Genome Taxonomy Database, is stable for a range of phylogenetic variables including marker gene selection, inference methods, corrections for rate heterogeneity and compositional bias, tree rooting scenarios and expansion of the genome database. Rank normalization is shown to robustly correct for substitution rates varying up to 30-fold using simulated datasets. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes while taking into account proposals to formally recognize the rank of phylum and to use genome sequences as type material. This taxonomy is based on 2,392 archaeal genomes, 93.3% of which required one or more changes to their existing taxonomy, mainly owing to incomplete classification. We identify 16 archaeal phyla and reclassify 3 major monophyletic units from the former Euryarchaeota and one phylum that unites the Thaumarchaeota-Aigarchaeota-Crenarchaeota-Korarchaeota (TACK) superphylum into a single phylum.

Genera specific distribution of DEAD-box RNA helicases in cyanobacteria.

Although RNA helicases are essentially ubiquitous and perform roles in all stages of RNA metabolism, phylogenetic analysis of the DEAD (Asp-Glu-Ala-Asp)-box RNA helicase family in a single phylum has not been performed. Here, we performed a phylogenetic analysis on DEAD-box helicases from all currently available cyanobacterial genomes, comprising a total of 362 helicase protein sequences from 280 strains. DEAD-box helicases belonging to three distinct clades were observed. Two clades, the CsdA (cold shock DEAD-box A)-like and RhlE (RNA helicase E)-like helicases, cluster with the homologous proteins from Escherichia coli . The third clade, the CrhR (cyanobacterial RNA helicase Redox)-like helicases, is unique to cyanobacteria and characterized by a conserved sequence motif in the C-terminal extension. Restricted distribution is observed across cyanobacterial diversity with respect to both helicase type and strain. CrhR-like and CsdA-like helicases essentially never occur together, while RhlE always occurs with either a CrhR-like or CsdA-like helicase. CrhR-like and RhlE-like proteins occurred in filamentous cyanobacteria of the orders Nostocales , Oscillatoriales and Synechococcales . Similarly, CsdA- and RhlE-like proteins are restricted to unicellular cyanobacteria of the genera Cyanobium and Synechococcus . In addition, the unexpected occurrence of RhlE in two Synechococcus strains suggests recent acquisition and evolutionary divergence. This study, therefore, raises physiological and evolutionary questions as to why DEAD-box RNA helicases encoded in cyanobacterial lineages display restricted distributions, suggesting niches that require either CrhR or CsdA RNA helicase activity but not both. Extensive conservation of gene synteny surrounding the previously described rimO–crhR operon is also observed, indicating a role in the maintenance of photosynthesis. The analysis provides insights into the evolution, origin and dissemination of sequences within a single gene family to yield divergent functional roles.

The Bacterial Communities of Little Cigars and Cigarillos Are Dynamic Over Time and Varying Storage Conditions.

Despite their potential importance with regard to tobacco-related health outcomes, as well as their hypothesized role in the production of tobacco-specific N-nitrosamines, bacterial constituents of tobacco products lack characterization. Specifically, to our knowledge, there has been no comprehensive characterization of the effects of storage conditions on the bacterial communities associated with little cigars and cigarillos. To address this knowledge gap, we characterized the bacterial community composition of the tobacco and wrapper components of the following four products: Swisher Sweets Original; Swisher Sweets, Sweet Cherry; Cheyenne Cigars Full Flavor 100’s; and Cheyenne Menthol Box. Each product was stored under three different conditions of temperature and relative humidity to mimic different user storage conditions: room (20°C 50% RH), refrigerator (5°C 18% RH) and pocket (25°C 30% RH). On days 0, 5, 9 and 14, subsamples were collected, the wrapper and tobacco were separated, and their total DNA was extracted separately and purified. Resulting DNA was then used in PCR assays targeting the V3 V4 region of the bacterial 16S rRNA gene, followed by sequencing using Illumina HiSeq 300bp PE. Resulting sequences were processed using the Quantitative Insights Into Microbial Ecology (QIIME) software package, followed by analyses in R using the Phyloseq and Vegan packages. A single bacterial phylum, Firmicutes, dominated in the wrapper subsamples whereas the tobacco subsamples were dominated by Proteobacteria. Cheyenne Menthol Box (CMB) samples were characterized by significant differential abundances for 23 bacterial operational taxonomic units (OTUs) in tobacco subsamples and 27 OTUs in the wrapper subsamples between day 0 and day 14 under all conditions. OTUs from the genera Acinetobacter and Bacillus significantly increased in the CMB tobacco subsamples, and OTUs from Bacillus, Streptococcus, Lactobacillus, and Enterococcus significantly increased in the CMB wrapper subsamples over time. These initial results suggest that the bacterial communities of little cigars and cigarillos are dynamic over time and varying storage conditions.

Characterization of Microbial Communities Populating the Inflorescences of Humulus lupulus L.

The aerial portion of plants (phyllosphere) harbors complex and diverse microbial communities that have been shown to influence host growth and fitness, tolerance to environmental stressors, disease susceptibility, and the productivity of economically significant crops. However, despite its reproductive importance to the host and economic value, the microbial ecology of anatomical flowers (anthosphere) remains largely uninvestigated. Here a culture-independent assessment of bacterial communities on freshly harvested and dried inflorescences of eight hop varieties (Humulus lupulus L.), using Illumina MiSeq 16S platform-based rRNA gene sequence analysis, is reported. The results reveal the hops anthosphere is dominated by a single taxonomic phylum, the Proteobacteria, where at least 60% of the sequences are attributed across two genera, Pseudomonas (Gammaproteobacteria) and Sphingomonas (Alphaproteobacteria). Chao1 diversity analysis indicated the presence of many very rare taxa across all varieties. Beta-diversity analysis resolved, from the comparison of unweighted and weighted UniFrac distances, the absence of distinct clustering between freshly harvested and dried hops or between hop varieties. The prevalence of Proteobacteria associated with hop inflorescences is consistent with other anthosphere microbiomes; however, presently the predominance of Gammaproteobacteria in the phyllosphere appears to be a distinct characteristic of the hops microbiome.

Evaluating the diversity and composition of bacterial communities associated with Vachellia pachyceras - the only existing native tree species in the Kuwait desert.

We investigated the diversity and composition of bacterial communities in rhizospheric and non-rhizospheric bulk soils as well as root nodule bacterial communities of Vachellia pachyceras - the only native tree species existing in the Kuwait desert. Community fingerprinting comparisons and 16S rDNA sequence identifications were used for characterization of the bacterial population using specific primers. The bacterial characterization of soil samples revealed four major phyla: Acidobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. In situ (desert) samples of both rhizospheric and non-rhizospheric bulk soil were dominated by the bacterial phyla Firmicutes and Bacteroidetes, whereas the phylum Betaproteobacteria was present only in non-rhizospheric bulk soil. Ex situ (nursery growing condition) V. pachyceras resulted in restricted bacterial communities dominated by members of a single phylum, Bacteroidetes. Results indicated that the soil organic matter and rhizospheric environments might drive the bacterial community. Despite harsh climatic conditions, data demonstrated that V. pachyceras roots harbor endophytic bacterial populations. Our findings on bacterial community composition and structure have major significance for evaluating how Kuwait's extreme climatic conditions affect bacterial communities. The baseline data obtained in this study will be useful and assist in formulating strategies in ecological restoration programs, including the application of inoculation technologies.

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.

Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.

High-throughput sequencing reveals microbial communities in drinking water treatment sludge from six geographically distributed plants, including potentially toxic cyanobacteria and pathogens

The microbial community structures of drinking water treatment sludge (DWTS) generated for raw water (RW) from different locations and with different source types — including river water, lake water and reservoir water —were investigated using high-throughput sequencing. Because the unit operations in the six DWTPs were similar, community composition in fresh sludge may be determined by microbial community in the corresponding RW. Although Proteobacteria, Cyanobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, and Planctomycetes were the dominant phyla among the six DWTS samples, no single phylum exhibited similar abundance across all the samples, owing to differences in total phosphorus, chemical oxygen demand, Al, Fe, and chloride in RW. Three genera of potentially toxic cyanobacteria (Planktothrix, Microcystis and Cylindrospermopsis), and four potential pathogens (Escherichia coli, Bacteroides ovatus, Prevotella copri and Rickettsia) were found in sludge samples. Because proliferation of potentially toxic cyanobacteria and Rickettsia in RW was mainly affected by nutrients, while growth of Escherichia coli, Bacteroides ovatus and Prevotella copri in RW may be influenced by Fe, control of nutrients and Fe in RW is essential to decrease toxic cyanobacteria and pathogens in DWTS.

A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data

Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopagomycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed.

Impact of nitrogen and phosphorus on phytoplankton production and bacterial community structure in two stratified Antarctic lakes: a bioassay approach

Arctic, Antarctic, and alpine ecosystems are recognized as sensors and sentinels of global change. As a consequence of their high sensitivity to minor climatic perturbations, permanently ice-covered lakes located in the McMurdo Dry Valleys (MDV), Antarctica, represent end members in the global network of inland bodies of water. Episodic climatic events in the form of increased summer glacial melt result in inputs of organic sediment and nutrients from glacial streams to these closed basins. Phytoplankton communities residing in the oligotrophic water columns are highly responsive to pulses in nutrient availability; however, there is a lack of understanding on whether specific phytoplankton groups are more competitive during a summer flood event and how shifts in the phytoplankton community may influence heterotrophic bacteria. A bioassay approach in 3-l bottles was used to investigate the influence of inorganic nitrogen and phosphorus availability on planktonic communities from the oligotrophic upper waters of two chemically distinct MDV lakes (Lakes Bonney and Fryxell) which differ in their external inputs and water column N/P stoichiometry. While microbial community responses varied between lakes and were nutrient-dependent, stimulation of phytoplankton biomass and productivity across all treatments was strongly linked with increased abundance of a single phytoplankton phylum (Chlorophyta). Despite stimulation of phytoplankton growth, primary and bacterial productivity was generally uncoupled; however, shifts in bacterial community diversity were observed in bioassays amended with either P or NP. We suggest that climate-associated increases in phytoplankton production and concomitant shifts in diversity will influence MDV bacterial community structure by altering the availability and composition of autochthonous carbon for heterotrophic production.

Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage.

Recent studies have expanded the phylum Chlorobi, demonstrating that the green sulfur bacteria (GSB), the original cultured representatives of the phylum, are a part of a broader lineage whose members have more diverse metabolic capabilities that overlap with members of the phylum Bacteroidetes. The 16S rRNA gene of an uncultivated clone, OPB56, distantly related to the phyla Chlorobi and Bacteroidetes, was recovered from Obsidian Pool in Yellowstone National Park; however, the detailed phylogeny and function of OPB56 and related clones have remained unknown. Culturing of thermophilic bacterial consortia from compost by adaptation to grow on ionic-liquid pretreated switchgrass provided a consortium in which one of the most abundant members, NICIL-2, clustered with OPB56-related clones. Phylogenetic analysis using the full-length 16S rRNA gene from NICIL-2 demonstrated that it was part of a monophyletic clade, referred to as OPB56, distinct from the Bacteroidetes and Chlorobi. A near complete draft genome (>95% complete) was recovered from metagenomic data from the culture adapted to grow on ionic-liquid pretreated switchgrass using an automated binning algorithm, and this genome was used for marker gene-based phylogenetic analysis and metabolic reconstruction. Six additional genomes related to NICIL-2 were reconstructed from metagenomic data sets obtained from thermal springs at Yellowstone National Park and Nevada Great Boiling Spring. In contrast to the 16S rRNA gene phylogenetic analysis, protein phylogenetic analysis was most consistent with the clustering of the Chlorobea, Ignavibacteria and OPB56 into a single phylum level clade. Metabolic reconstruction of NICIL-2 demonstrated a close linkage with the class Ignavibacteria and the family Rhodothermaceae, a deeply branching Bacteroidetes lineage. The combined phylogenetic and functional analysis of the NICIL-2 genome has refined the membership in the phylum Chlorobi and emphasized the close evolutionary and metabolic relationship between the phyla Chlorobi and the Bacteroidetes.

Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites.

BackgroundHomopolymeric tracts, particularly poly dA.dT, are enriched within the intergenic sequences of eukaryotic genomes where they appear to act as intrinsic regulators of nucleosome positioning. A previous study of the incomplete genome of the human malarial parasite Plasmodium falciparum reports a higher than expected enrichment of poly dA.dT tracts, far above that anticipated even in this highly AT rich genome. Here we report an analysis of the relative frequency, length and spatial arrangement of homopolymer tracts for the complete P. falciparum genome, extending this analysis to twelve additional genomes of Apicomplexan parasites important to human and animal health. In addition, using nucleosome-positioning data available for P. falciparum, we explore the correlation of poly dA.dT tracts with nucleosome-positioning data over key expression landmarks within intergenic regions.ResultsWe describe three apparent lineage-specific patterns of homopolymeric tract organization within the intergenic regions of these Apicomplexan parasites. Moreover, a striking pattern of enrichment of overly long poly dA.dT tracts in the intergenic regions of Plasmodium spp. uniquely extends into protein coding sequences. There is a conserved spatial arrangement of poly dA.dT immediately flanking open reading frames and over predicted core promoter sites. These key landmarks are all relatively depleted in nucleosomes in P. falciparum, as would be expected for poly dA.dT acting as nucleosome exclusion sequences.ConclusionsPrevious comparative studies of homopolymer tract organization emphasize evolutionary diversity; this is the first report of such an analysis within a single phylum. Our data provide insights into the evolution of homopolymeric tracts and the selective pressures at play in their maintenance and expansion.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-848) contains supplementary material, which is available to authorized users.

The urbilaterian brain revisited: novel insights into old questions from new flatworm clades.

Flatworms are classically considered to represent the simplest organizational form of all living bilaterians with a true central nervous system. Based on their simple body plans, all flatworms have been traditionally grouped together in a single phylum at the base of the bilaterians. Current molecular phylogenomic studies now split the flatworms into two widely separated clades, the acoelomorph flatworms and the platyhelminth flatworms, such that the last common ancestor of both clades corresponds to the urbilaterian ancestor of all bilaterian animals. Remarkably, recent comparative neuroanatomical analyses of acoelomorphs and platyhelminths show that both of these flatworm groups have complex anterior brains with surprisingly similar basic neuroarchitectures. Taken together, these findings imply that fundamental neuroanatomical features of the brain in the two separate flatworm groups are likely to be primitive and derived from the urbilaterian brain.

Genomic distribution and heterogeneity of MocR-like transcriptional factors containing a domain belonging to the superfamily of the pyridoxal-5′-phosphate dependent enzymes of fold type I

Bacterial proteins belonging to the MocR/GabR family are chimeric proteins incorporating a short N-terminal helix-turn-helix containing domain with DNA-binding properties, and a long C-terminal domain belonging to the superfamily of the pyridoxal-5′-phosphate enzymes of fold type I. The first purpose of this report is to give an overview of the distribution of these factors among the different taxonomical bacterial divisions and to determine the degree of conservation of the main structural features of the PLP binding domain. Complete proteomes of bacteria phyla were scanned with a hidden Markov model representative of the MocR family. Results indicate that presence of MocR factors is heterogeneous even within the single bacterial phylum: some species miss completely the factors, while others possess one or even more regulators. Absence of MocR factors is distinctive of some phyla such as Chlamydiae. The genomic distribution of MocR is, as expected, highly correlated to the size of the genome. At variance, phyla missing MocR regulators generally are characterized by compact genomes, of the order of 1.0–2.0Mb, such as the case of Mollicutes or Chlamydiae. Apparently, the minimum genome size compatible with the presence of MocR genes is around 2.0–2.5Mb. Conservation of the residues corresponding to those involved in the interaction with the cofactor pyridoxal-5′-phosphate in the homologous 2-aminoadipate aminotransferase, was analyzed in the multiple sequence alignments of MocR within each phyla considered. In the vast majority of cases, residues are conserved or conservatively replaced. This result suggests that, in most cases, MocR factors preserve at least ability to bind the cofactor and very likely some catalytic abilities.

On velvet worms and caterpillars: Science, fiction, or science fiction?

Velvet worms (phylum Onychophora) are fascinating animals. Their colored velvety skin and glue-shooting organs attract the attention of nature lovers. Their geographical distribution across the former Gondwana fascinates biogeographers. Onychophora is also the single animal phylum with a strictly terrestrial distribution. And their abundant Cambrian fossil record has greatly inspired paleontologists. A new claim, however, published by D. I. Williamson (1) makes them even more fascinating. This proposal makes onychophorans the evolutionary source of insect caterpillars—after their adult insect genome hybridized with that of a velvet worm. The matter appears extracted from a science fiction novel but has grave implications. … 1E-mail: ggiribet{at}oeb.harvard.edu

A one ocean model of biodiversity

Abstract The history of life is written in the ocean, and the history of the ocean is written in DNA. Geologists have shown us that hundreds of millions of years of ocean history can be revealed from records of a single phylum in cores of mud from abyssal plains. We are now accumulating genetic tools to unravel the relationships of hundreds of phyla to track this history back billions of years. The technologies demonstrated by the Census of Marine Life (CoML) mean that the ocean is no longer opaque or unknowable. The secrets of the largest component of the biosphere are knowable. The cost of understanding the history of ocean life is not cheap, but it is also not prohibitive. A transparent, open ocean is available for us to use to understand ourselves. This article develops a model of biodiversity equilibration in a single, physically static ocean as a step towards biodiversity in physically complex real oceans. It attempts to be quantitative and to simultaneously account for biodiversity patterns from bacteria to whales focusing on emergent properties rather than details. Biodiversity reflects long-term survival of DNA sequences, stabilizing “ecosystem services” despite environmental change. In the ocean, mechanisms for ensuring survival range from prokaryotes maintaining low concentrations of replicable DNA throughout the ocean volume, anticipating local change, to animals whose mobility increases with mass to avoid local change through movement. Whales can reach any point in the ocean in weeks, but prokaryotes can only diffuse. The high metabolic costs of mobility are offset by the dramatically lower number of DNA replicates required to ensure survival. Reproduction rates probably scale more or less inversely with body mass. Bacteria respond in a week, plankton in a year, whales in a century. We generally lack coherent theories to explain the origins of animals (metazoans) and the contributions of biodiversity to ecosystems. The One Ocean Model suggests that mobile metazoans paved the way for their own energetic life styles by decreasing the amount of primary production sinking to feed the benthic anaerobic prokaryotes. Increasing metazoan mobility and diversity ensured that less and less production sank and accelerated development of the aerobic oceans they require. High biodiversity among middle-sized organisms stabilizes the system, but rapid environmental changes can decrease diversity in a positive feedback loop ending in mass extinction events and the return of the anaerobes. The oceans have gone through this cycle several times. Global warming may be a mild flu compared to “the revenge of the microbes”.

Verrucomicrobia Joining the Proteasome Club

In eukaryotes, the proteasome represents the major system for controlled intracellular proteolysis. Its ubiquitin-independent counterpart in prokaryotes is structurally well characterized, but still little is known about its cellular targets and hence its physiological role (M. J. Pearce, P. Arora, R. A. Festa, S. M. Butler-Wu, R. S. Gokhale, and K. H. Darwin, EMBO J. 25:5423, 2006; S. Gandotra S, D. Schnap-pinger, M. Monteleone, W. Hillen, and S. Ehrt, Nature Med. 13:1515, 2008). From an evolutionary point of view, this compartmentalized protease is also of interest as a possible ancestor of the eukaryotic system (R. E. Valas and P. E. Bourne, J. Mol. Evol. 66:494, 2008). Although widespread in Archaea, occurrence of the 20S proteasome (28-subunit barrel-shaped proteolytic core) appeared to be confined to a single phylum of gram-positive bacteria, the Actinobacteria, including genera like Mycobacterium, Rhodococcus, and Streptomyces. Recently, this viewpoint needed adjustment upon proteogenomic identification in mine-drainage biofilm of actinomycete-like proteasomes from uncultivated Leptospirilla, acidophilic gram-negative bacteria of the Nitrospirae phylum (R. De Mot, Trends Microbiol. 15: 335, 2007). Now, genomic data for two cultivated soil isolates of the equally poorly characterized phylum Verrucomicrobia reveal that equivalents of the characteristic six-gene cluster previously identified in Leptospirillum (mpa-pafX-orfX-prcB-prcA-pafA) are present in the extremely acidophilic methanotroph ‘Methylacidiphilum infernorum’ V4 (P. F. Dunfield et al., Nature 450:879; GenBank CP000975) and the xylan-utilizing strain Ellin514 (P. Sangwan, S. Kovac, K. E. Davis, M. Sait, and P. H. Janssen, Appl. Environ. Microbiol. 71:8402, 2005; Gen-Bank ABOX010000075). The moderate level of homology between the respective verrucomicrobial orthologues (46–54 % amino acid identity) and significant difference in G + C-content of the gene clusters (10%) reflect the different subdivision affiliation of these strains within the phylum. Much like the two Leptospirillum proteasome gene clusters, the genome context of both verrucomicrobial clusters is not conserved and lacks synteny with flanking genes in actinomycete genomes.

First Molecular Data on the Phylum Loricifera – An Investigation into the Phylogeny of Ecdysozoa with Emphasis on the Positions of Loricifera and Priapulida

Recent progress in molecular techniques has generated a wealth of information for phylogenetic analysis. Among metazoans all but a single phylum have been incorporated into some sort of molecular analysis. However, the minute and rare species of the phylum Loricifera have remained elusive to molecular systematists. Here we report the first molecular sequence data (nearly complete 18S rRNA) for a member of the phylum Loricifera, Pliciloricus sp. from Korea. The new sequence data were analyzed together with 52 other ecdysozoan sequences, with all other phyla represented by three or more sequences. The data set was analyzed using parsimony as an optimality criterion under direct optimization as well as using a Bayesian approach. The parsimony analysis was also accompanied by a sensitivity analysis. The results of both analyses are largely congruent, finding monophyly of each ecdysozoan phylum, except for Priapulida, in which the coelomate Meiopriapulus is separate from a clade of pseudocoelomate priapulids. The data also suggest a relationship of the pseudocoelomate priapulids to kinorhynchs, and a relationship of nematodes to tardigrades. The Bayesian analysis placed the arthropods as the sister group to a clade that includes tardigrades and nematodes. However, these results were shown to be parameter dependent in the sensitivity analysis. The position of Loricifera was extremely unstable to parameter variation, and support for a relationship of loriciferans to any particular ecdysozoan phylum was not found in the data.

Taxonomic distinctness as a measure of diversity applied over a large scale: the benthos of the Norwegian continental shelf

Summary Data on soft‐sediment macrobenthos from the Norwegian continental shelf (56–71°N) was used to examine the use of average taxonomic distinctness (Δ+, a measure of the average degree to which species are related to each other) as a diversity measure. Δ+ for all taxa combined decreased with both latitude and depth. In contrast Δ+ for annelids and crustaceans (71% of the fauna) was positively correlated to latitude and depth, whereas molluscs (20·1% of the fauna) were not related to latitude or depth. Depth explained most of the variance in Δ+ for annelids and crustaceans. Neither latitude nor grain size appeared to be important in explaining large‐scale patterns in the taxonomic breadth of the three dominant phyla. In contrast latitude rather than depth explained most of the variance in Δ+ of all taxa combined. The finding that molluscs showed different patterns of Δ+ than the two other dominant phyla shows that the biodiversity of different phyla responded differently to environmental gradients and that one phylum cannot be used as a surrogate for others in such studies. The most likely explanation for the inconsistency in Δ+ is because the taxonomic classification system also varies between different phyla, and taxonomically related biodiversity measures might be more meaningfully applied to a single phylum than to all taxa combined. Δ+ and species richness (S) displayed different patterns of biodiversity. Thus Δ+ is not a surrogate for species richness. Species richness of all taxa combined and annelids were highest in the middle depth range, and lowest in the shallowest and deepest parts of the shelf. Most of the variance in species richness is accounted for by depth, followed by latitude and grain size for all three dominant phyla and all taxa combined.