Complete genome sequence of Leadbetterella byssophila type strain (4M15)

Interplay between the microalgae Micrasterias radians and its symbiont Dyadobacter sp. HH091

Based on previous research, related to detailed insight into mutualistic collaboration of microalga and its microbiome, we established an artificial plant-bacteria system of the microalga Micrasterias radians MZCH 672 and the bacterial isolate Dyadobacter sp. HH091. The bacteria, affiliated with the phylum Bacteroidota, strongly stimulated growth of the microalga when it was added to axenic algal cultures. For further advances, we studied the isolate HH091 and its interaction with the microalga M. radians using transcriptome and extensive genome analyses. The genome of HH091 contains predicted polysaccharide utilizing gene clusters co-working with the type IX secretion system (T9SS) and conceivably involved in the algae-bacteria liaison. Here, we focus on characterizing the mechanism of T9SS, implementing the attachment and invasion of microalga by Dyadobacter sp. HH091. Omics analysis exposed T9SS genes: gldK, gldL, gldM, gldN, sprA, sprE, sprF, sprT, porU and porV. Besides, gld genes not considered as the T9SS components but required for gliding motility and protein secretion (gldA, gldB, gldD, gldF, gldG, gldH, gldI, gldJ), were also identified at this analysis. A first model of T9SS apparatus of Dyadobacter was proposed in a course of this research. Using the combination of fluorescence labeling of Dyadobacter sp. HH091, we examined the bacterial colonisation and penetration into the cell wall of the algal host M. radians MZCH 672.

Identification of nitrogen-incorporating bacteria in a sequencing batch reactor: A combining cultivation-dependent and cultivation-independent method

Nitrogen-incorporating bacteria in activated sludge play important roles in nitrogen removal in sequencing bactch reactor (SBR), but the active microorganisms and their interactions in the complex community are rarely revealed. Herein, a combining cultivation-dependent and cultivation-independent methods associated with DNA-stable-isotope probing (SIP) was applied to determine the microbes responsible for nitrogen-incorporating in SBR. Results revealed that Cytophagaceae and Sphingobacteriales were identified to be involved in nitrification, and Anaerolineae, Plasticicumulans and Elusimicrobia were responsible for denitrification. Cultivable nitrobacter and denitrifiers were isolated from the activated sludge, but they did not participate in the nitrogen-incorporating based on the SIP results. Additionally, the molecular ecological network analysis indicated that the SIP-identified nitrogen-incorporating bacteria exhibited more links with the intra-community, which might explain the failure of isolating these active bacteria. These findings add understanding of the removal of nitrogenous compounds drived by nitrogen-incorporating bacteria in actual wastewater treatment process.

Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots

Seagrass roots host a diverse microbiome that is critical for plant growth and health. Composition of microbial communities can be regulated in part by root exudates, but the specifics of these interactions in seagrass rhizospheres are still largely unknown. As light availability controls primary productivity, reduced light may impact root exudation and consequently the composition of the root microbiome. Hence, we analyzed the influence of light availability on root exudation and community structure of the root microbiome of three co-occurring seagrass species, Halophila ovalis, Halodule uninervis and Cymodocea serrulata. Plants were grown under four light treatments in mesocosms for 2 weeks; control (100% surface irradiance (SI), medium (40% SI), low (20% SI) and fluctuating light (10 days 20% and 4 days 100%). 16S rDNA amplicon sequencing revealed that microbial diversity, composition and predicted function were strongly influenced by the presence of seagrass roots, such that root microbiomes were unique to each seagrass species. Reduced light availability altered seagrass root exudation, as characterized using fluorescence spectroscopy, and altered the composition of seagrass root microbiomes with a reduction in abundance of potentially beneficial microorganisms. Overall, this study highlights the potential for above-ground light reduction to invoke a cascade of changes from alterations in root exudation to a reduction in putative beneficial microorganisms and, ultimately, confirms the importance of the seagrass root environment - a critical, but often overlooked space.

Architecture, component, and microbiome of biofilm involved in the fouling of membrane bioreactors

Biofilm formation on the filtration membrane and the subsequent clogging of membrane pores (called biofouling) is one of the most persistent problems in membrane bioreactors for wastewater treatment and reclamation. Here, we investigated the structure and microbiome of fouling-related biofilms in the membrane bioreactor using non-destructive confocal reflection microscopy and high-throughput Illumina sequencing of 16S rRNA genes. Direct confocal reflection microscopy indicated that the thin biofilms were formed and maintained regardless of the increasing transmembrane pressure, which is a common indicator of membrane fouling, at low organic-loading rates. Their solid components were primarily extracellular polysaccharides and microbial cells. In contrast, high organic-loading rates resulted in a rapid increase in the transmembrane pressure and the development of the thick biofilms mainly composed of extracellular lipids. High-throughput sequencing revealed that the biofilm microbiomes, including major and minor microorganisms, substantially changed in response to the organic-loading rates and biofilm development. These results demonstrated for the first time that the architectures, chemical components, and microbiomes of the biofilms on fouled membranes were tightly associated with one another and differed considerably depending on the organic-loading conditions in the membrane bioreactor, emphasizing the significance of alternative indicators other than the transmembrane pressure for membrane biofouling.

Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls

Sinking of large organic food falls i.e. kelp, wood and whale carcasses to the oligotrophic deep-sea floor promotes the establishment of locally highly productive and diverse ecosystems, often with specifically adapted benthic communities. However, the fragmented spatial distribution and small area poses challenges for the dispersal of their microbial and faunal communities. Our study focused on the temporal dynamics and spatial distributions of sunken wood bacterial communities, which were deployed in the vicinity of different cold seeps in the Eastern Mediterranean and the Norwegian deep-seas. By combining fingerprinting of bacterial communities by ARISA and 454 sequencing with in situ and ex situ biogeochemical measurements, we show that sunken wood logs have a locally confined long-term impact (> 3y) on the sediment geochemistry and community structure. We confirm previous hypotheses of different successional stages in wood degradation including a sulphophilic one, attracting chemosynthetic fauna from nearby seep systems. Wood experiments deployed at similar water depths (1100-1700 m), but in hydrographically different oceanic regions harbored different wood-boring bivalves, opportunistic faunal communities, and chemosynthetic species. Similarly, bacterial communities on sunken wood logs were more similar within one geographic region than between different seas. Diverse sulphate-reducing bacteria of the Deltaproteobacteria, the sulphide-oxidizing bacteria Sulfurovum as well as members of the Acidimicrobiia and Bacteroidia dominated the wood falls in the Eastern Mediterranean, while Alphaproteobacteria and Flavobacteriia colonized the Norwegian Sea wood logs. Fauna and bacterial wood-associated communities changed between 1 to 3 years of immersion, with sulphate-reducers and sulphide-oxidizers increasing in proportion, and putative cellulose degraders decreasing with time. Only 6% of all bacterial genera, comprising the core community, were found at any time on the Eastern Mediterranean sunken wooden logs. This study suggests that biogeography and succession play an important role for the composition of bacteria and fauna of wood-associated communities, and that wood can act as stepping-stones for seep biota.

Genome-Based Taxonomic Classification of Bacteroidetes

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.

Functional maintenance and structural flexibility of microbial communities perturbed by simulated intense rainfall in a pilot-scale membrane bioreactor

Intense rainfall is one of the most serious and common natural events, causing the excessive inflow of rainwater into wastewater treatment plants. However, little is known about the impacts of rainwater dilution on the structure and function of the sludge microorganisms. Here, high-throughput sequencing of 16S ribosomal RNA (rRNA) genes was implemented to describe the microbial community dynamics during the simulated intense rainfall situation (event i) in which approximately 45 % of the sludge biomass was artificially overflowed by massive water supply in a pilot-scale membrane bioreactor. Thereafter, we investigated the functional and structural responses of the perturbed microbial communities to subsequent conditional changes, i.e., an increase in organic loading rate from 225 to 450 mg chemical oxygen demand (COD) l(-1) day(-1) (event ii) and an addition of a microbiota activator (event iii). Due to the event i, the COD removal declined to 78.2 %. This deterioration coincided with the decreased microbial diversity and the proliferation of the oligotrophic Aquabacterium sp. During the succeeding events ii and iii, the sludge biomass increased and the COD removal became higher (86.5-97.4 %). With the apparent recovery of the reactor performance, microbial communities became diversified and the compositions dynamically changed. Notably, various bacterial micropredators were highly enriched under the successive conditions, most likely being involved in the flexible reorganization of microbial communities. These results indicate that the activated sludge harbored functionally redundant microorganisms that were able to thrive and proliferate along with the conditional changes, thereby contributing to the functional maintenance of the membrane bioreactor.

Evaluation of functional microbial community's difference in full-scale and lab-scale anaerobic digesters feeding with different organic solid waste: Effects of substrate and operation factors

Samples taken from the full-scale and lab-scale anaerobic digesters feeding with different organic solid waste were investigated with assessment of the substrate effects. To understand the substrate effects on the microbial community diversity, heterogeneity, and functional structure, twelve samples were analyzed by constructing 16S rRNA gene clone libraries and statistical analysis. Microbial diversity varied according to substrate types and operating parameters. With acetoclastic methanogen of genus Methanosaeta predominated in full scale and Methanosarcina predominated in the lab-scale digesters, a significant difference archaeal communities were found. Principal component analysis clearly indicates that both bacterial and archaeal communities create independent clusters according to substrate types. However, the relationship between acetogenic bacteria and the acetoclastic methanogens had a similar variation tends in most of full-scale and lab-scale reactors. Canonical correlation analysis and variance partitioning analysis implied that bacterial and archaeal community variations were significantly affected by substrate and the operation conditions.

Draft Genome Sequence of Cellulose-Digesting Bacterium Sporocytophaga myxococcoides PG-01

Sporocytophaga myxococcoides, a Gram-negative bacterium isolated from soil, is an efficient hydrolyzer of crystalline cellulose. Here, we report its draft genome sequence, which may provide important genetic information regarding the cellulolytic and hemicellulolytic enzymes that contribute to the cellulose-degrading abilities of this bacterium.

Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation

Although recent nucleotide sequencing technologies have significantly enhanced our understanding of microbial genomes, the function of ∼35% of genes identified in a genome currently remains unknown. To improve the understanding of microbial genomes and consequently of microbial processes it will be crucial to assign a function to this "genomic dark matter." Due to the urgent need for additional carbohydrate-active enzymes for improved production of transportation fuels from lignocellulosic biomass, we screened the genomes of more than 5,500 microorganisms for hypothetical proteins that are located in the proximity of already known cellulases. We identified, synthesized and expressed a total of 17 putative cellulase genes with insufficient sequence similarity to currently known cellulases to be identified as such using traditional sequence annotation techniques that rely on significant sequence similarity. The recombinant proteins of the newly identified putative cellulases were subjected to enzymatic activity assays to verify their hydrolytic activity towards cellulose and lignocellulosic biomass. Eleven (65%) of the tested enzymes had significant activity towards at least one of the substrates. This high success rate highlights that a gene context-based approach can be used to assign function to genes that are otherwise categorized as "genomic dark matter" and to identify biomass-degrading enzymes that have little sequence similarity to already known cellulases. The ability to assign function to genes that have no related sequence representatives with functional annotation will be important to enhance our understanding of microbial processes and to identify microbial proteins for a wide range of applications.

Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T))

Runella slithyformis Larkin and Williams 1978 is the type species of the genus Runella, which belongs to the Cytophagaceae, a family that was only recently classified to the order Cytophagales in the class Cytophagia. The species is of interest because it is able to grow at temperatures as low as 4°C. This is the first completed genome sequence of a member of the genus Runella and the sixth sequence from the family Cytophagaceae. The 6,919,729 bp long genome consists of a 6.6 Mbp circular genome and five circular plasmids of 38.8 to 107.0 kbp length, harboring a total of 5,974 protein-coding and 51 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Complete genome sequence of Odoribacter splanchnicus type strain (1651/6)

Odoribacter splanchnicus (Werner et al. 1975) Hardham et al. 2008 is the type species of the genus Odoribacter, which belongs to the family Porphyromonadaceae in the order 'Bacteroidales'. The species is of interest because members of the Odoribacter form an isolated cluster within the Porphyromonadaceae. This is the first completed genome sequence of a member of the genus Odoribacter and the fourth sequence from the family Porphyromonadaceae. The 4,392,288 bp long genome with its 3,672 protein-coding and 74 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.