Viable cytophaga-like bacterium in the 0.2 microm-filtrate seawater

Size Matters: Ultra-small and Filterable Microorganisms in the Environment

Ultra-small microorganisms are ubiquitous in Earth’s environments. Ultramicrobacteria, which are defined as having a cell volume of <0.1 μm³, are often numerically dominant in aqueous environments. Cultivated representatives among these bacteria, such as members of the marine SAR11 clade (e.g., “Candidatus Pelagibacter ubique”) and freshwater Actinobacteria and Betaproteobacteria, possess highly streamlined, small genomes and unique ecophysiological traits. Many ultramicrobacteria may pass through a 0.2-μm-pore-sized filter, which is commonly used for filter sterilization in various fields and processes. Cultivation efforts focusing on filterable small microorganisms revealed that filtered fractions contained not only ultramicrocells (i.e., miniaturized cells because of external factors) and ultramicrobacteria, but also slender filamentous bacteria sometimes with pleomorphic cells, including a special reference to members of Oligoflexia, the eighth class of the phylum Proteobacteria. Furthermore, the advent of culture-independent “omics” approaches to filterable microorganisms yielded the existence of candidate phyla radiation (CPR) bacteria (also referred to as “Ca. Patescibacteria”) and ultra-small members of DPANN (an acronym of the names of the first phyla included in this superphyla) archaea. Notably, certain groups in CPR and DPANN are predicted to have minimal or few biosynthetic capacities, as reflected by their extremely small genome sizes, or possess no known function. Therefore, filtered fractions contain a greater variety and complexity of microorganisms than previously expected. This review summarizes the broad diversity of overlooked filterable agents remaining in “sterile” (<0.2-μm filtered) environmental samples.

Oligoflexus tunisiensis gen. nov., sp. nov., a Gram-negative, aerobic, filamentous bacterium of a novel proteobacterial lineage, and description of Oligoflexaceae fam. nov., Oligoflexales ord. nov. and Oligoflexia classis nov

A phylogenetically novel proteobacterium, strain Shr3^T, was isolated from sand gravels collected from the eastern margin of the Sahara Desert. The isolation strategy targeted bacteria filterable through 0.2-µm-pore-size filters. Strain Shr3^T was determined to be a Gram-negative, aerobic, non-motile, filamentous bacterium. Oxidase and catalase reactions were positive. Strain Shr3^T showed growth on R2A medium, but poor or no growth on nutrient agar, trypticase soy agar and standard method agar. The major isoprenoid quinone was menaquinone-7. The dominant cellular fatty acids detected were C_16 : 1ω5c and C_16 : 0, and the primary hydroxy acid present was C_12 : 0 3-OH. The DNA G+C content was 54.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Shr3^T was affiliated with an uncultivated lineage of the phylum Proteobacteria; the nearest known type strain, with 83 % sequence similarity, was Desulfomicrobium orale DSM 12838^T in the class Deltaproteobacteria. The isolate and closely related environmental clones formed a novel class-level clade in the phylum Proteobacteria with high bootstrap support (96–99 %). Based on these results, the novel class Oligoflexia classis nov. in the phylum Proteobacteria and the novel genus and species Oligoflexus tunisiensis gen. nov., sp. nov. are proposed for strain Shr3^T, the first cultivated representative of the Oligoflexia. The type strain of Oligoflexus tunisiensis is Shr3^T ( = JCM 16864^T = NCIMB 14846^T). We also propose the subordinate taxa Oligoflexales ord. nov. and Oligoflexaceae fam. nov. in the class Oligoflexia.

Metagenomic analysis of 0.2-μm-passable microorganisms in deep-sea hydrothermal fluid

We pyrosequenced the bulk DNA extracted from microorganisms that passed through 0.2-μm-pore-size filters and trapped by 0.1-μm-pore-size filters in the hydrothermal fluid of the Mariana Trough. Using the 454-FLX sequencer, we generated 202,648 sequences with an average length of 173.8 bases. Functional profiles were assigned by the SEED Annotation Engine. In the metagenome of the 0.2-μm-passable microorganisms, genes related to membrane function, including potassium homeostasis classified as membrane transport, and multidrug-resistance efflux pumps classified as virulence, were dominant. There was a higher proportion of genes pertinent to the subsystem of membrane transport in our metagenomic library than in other oceanic and hydrothermal vent metagenomes. Genes associated with a RND-type efflux transporter for exogenous substances were specifically identified in the present study. After a comparative analysis with the genome of the known ultramicrobacterium Sphingopyxis alaskensis RB2256, we discovered 1,542 cases of significant hits (E < 1 × 10(-2)) in our metagenome, and 1,172 of those were related to the DNA repair protein RadA. In this way, the microbial functional profile of 0.2-μm-passable fraction in the present study differs from oceanic metagenomes in the 0.2-μm-trapped fractions and hydrothermal vent metagenomes reported in previous research.

Measurement of retention efficiency of filters against nanoparticles in liquids using an aerosolization technique

An aerosolization technique has been developed to measure liquid-borne nanoparticles down to 30 nm and applied to evaluate retention efficiencies of liquid filters. This technique involves dispersing nanoparticle suspensions into air-borne form and measuring the size and concentration by a differential mobility analyzer coupled to a condensation particle counter. Polystyrene latex particles larger and smaller than 70 nm in diameter were dispersed by a constant output atomizer, COA, and an electrospray aerosol generator, ES, respectively, to avoid the interference from residue particles. With the ES, residue particles can be controlled to be less than 10 nm, allowing latex particles as small as 30 nm to be clearly distinguished from the size distribution measurements. Calibrations with 30, 50, 125, and 200 nm latex particles showed that liquid-borne and air-borne particle concentrations are proportionally related. This provides an effective way to quantify liquid-borne particles as small as 30 nm, which cannot be analyzed by state-of-the-art liquid particle counters. An application of this technique is to evaluate the nanoparticle retention performance of liquid filters. Both 200 and 400 nm rated Nuclepore filters were challenged with latex particles of different sizes, and retention efficiency as a function of particle size was determined by comparing the particle concentrations upstream and downstream of the tested filters. The results are comparable with the nominal pore size stated by the manufacturer if sieving is the dominant filtration mechanism and demonstrate the feasibility of using the aerosolization technique to evaluate the retention efficiency of filters against nanoparticles in liquids.

Influence of size, shape, and flexibility on bacterial passage through micropore membrane filters

Sterilization of fluids by means of microfiltration is commonly applied in research laboratories as well as in pharmaceutical and industrial processes. Sterile micropore filters are subject to microbiological validation, where Brevundimonas diminuta is used as a standard test organism. However, several recent reports on the ubiquitous presence of filterable bacteria in aquatic environments have cast doubt on the accuracy and validity of the standard filter-testing method. Six different bacterial species of various sizes and shapes (Hylemonella gracilis, Escherichia coli, Sphingopyxis alaskensis, Vibrio cholerae, Legionella pneumophila, and B. diminuta) were tested for their filterability through sterile micropore filters. In all cases, the slender spirillum-shaped Hylemonella gracilis cells showed a superior ability to pass through sterile membrane filters. Our results provide solid evidence that the overall shape (including flexibility), instead of biovolume, is the determining factor for the filterability of bacteria, whereas cultivation conditions also play a crucial role. Furthermore, the filtration volume has a more important effect on the passage percentage in comparison with other technical variables tested (including flux and filter material). Based on our findings, we recommend a re-evaluation of the grading system for sterile filters, and suggest that the species Hylemonella should be considered as an alternative filter-testing organism for the quality assessment of micropore filters.

Quantification of the filterability of freshwater bacteria through 0.45, 0.22, and 0.1 microm pore size filters and shape-dependent enrichment of filterable bacterial communities

Micro-filtration is a standard process for sterilization in scientific research, medical, and industrial applications, and to remove particles in drinking water or wastewater treatment. It is generally assumed, and confirmed by quantifying filtration efficiency by plating, that filters with a 0.1-0.45 microm pore size can retain bacteria. In contrast to this assumption, we have regularly observed the passage of a significant fraction of natural freshwater bacterial communities through 0.45, 0.22, and 0.1 microm pore size filters. Flow cytometry and a regrowth assay were applied in the present study to quantify and cultivate filterable bacteria. Here we show for the first time a systematic quantification of their filterability, especially their ability to pass through 0.1 microm pore size filters. The filtered bacteria were subsequently able to grow on natural assimilable organic carbon (AOC) with specific growth rates up to 0.47 h(-1). We were able to enrich bacteria communities that pass preferentially through all three pore size filters at significantly increased percentages using successive filtration-regrowth cycles. In all instances, the dominant microbial populations comprised slender spirillum-shaped Hylemonella gracilis strains, suggesting shape-dependent selection during the filtration process. This quantification of the omnipresence of microfilterable bacterial in natural freshwater and their regrowth characteristics demand a change in the sterile filtration practice used in industrial and engineering applications as well as scientific research.

Phylotype diversity of deep-sea hydrothermal vent prokaryotes trapped by 0.2- and 0.1-microm-pore-size filters

Eleven 16S rRNA gene clone libraries including 34 archaeal and 72 bacterial phylotypes were constructed from total 708 clones of hydrothermal vent prokaryotes trapped by 0.2- and 0.1-microm-pore-size filters. Crenarchaeota and Proteobacteria phylotypes dominated the archaeal and bacterial populations, respectively. Novel unaffiliated phylotypes occurred only in the 0.1-microm-trapped populations.

The RgpB C-terminal domain has a role in attachment of RgpB to the outer membrane and belongs to a novel C-terminal-domain family found in Porphyromonas gingivalis

Porphyromonas gingivalis produces outer membrane-attached proteins that include the virulence-associated proteinases RgpA and RgpB (Arg-gingipains) and Kgp (Lys-gingipain). We analyzed the P. gingivalis outer membrane proteome and identified numerous proteins with C-terminal domains similar in sequence to those of RgpB, RgpA, and Kgp, indicating that these domains may have a common function. Using RgpB as a model to investigate the role of the C-terminal domain, we expressed RgpB as a full-length zymogen (recombinant RgpB [rRgpB]), with a catalytic Cys244Ala mutation [rRgpB(C244A)], or with the C-terminal 72 amino acids deleted (rRgpB435) in an Arg-gingipain P. gingivalis mutant (YH522AB) and an Arg- and Lys-gingipain mutant (YH522KAB). rRgpB was catalytically active and located predominantly attached to the outer membrane of both background strains. rRgpB(C244A) was inactive and outer membrane attached, with a typical attachment profile for both background strains according to sodium dodecyl sulfate-polyacrylamide gel electrophoresis, but in YH522KAB, the prodomain was not removed. Thus, in vivo, RgpB export and membrane attachment are independent of the proteolytic activity of RgpA, RgpB, or Kgp. However, for maturation involving proteolytic processing of RgpB, the proteolytic activity of RgpB, RgpA, or Kgp is required. The C-terminally-truncated rRgpB435 was not attached to the outer membrane and was located as largely inactive, discrete 71-kDa and 48-kDa isoforms in the culture supernatant and the periplasm. These results suggest that the C-terminal domain is essential for outer membrane attachment and may be involved in a coordinated process of export and attachment to the cell surface.

Phylogenetic characterization of 16S rRNA gene clones from deep-groundwater microorganisms that pass through 0.2-micrometer-pore-size filters

A total of 247 clones of 16S rRNA genes from microorganisms captured by 0.2- and 0.1-microm-pore-size filters from sedimentary and granite rock aquifers were amplified and yielded 37 operational taxonomic units (OTUs). Fifteen OTUs captured by 0.1-microm-pore-size filters were affiliated with the candidate divisions OD1 and OP11, representing novel lineages. On the other hand, OTUs captured by 0.2-microm-pore-size filters were largely affiliated with Betaproteobacteria.