Soil microbial functional gene dataset associated with Agathis australis.

Agathis australis (New Zealand kauri) is a significant and iconic native tree of Aotearoa New Zealand. Currently, Phytophthora agathidicida that causes kauri-dieback disease is killing kauri trees. Only 1% of the New Zealand virgin kauri forest remains [1,2]. Recent studies revealed that many soil-borne microorganisms had been found to systemically boost the defensive capacity of the trees by providing competition to pathogens for nutrient intake, thus preventing pathogen colonization and modulating plant immunity [3,4]. In addition, the root microbiome consists of an entire complex rhizosphere-associated microbes with their genetic elements and interactions that have influenced plant health. To date, very few studies have been conducted to investigate the microorganisms in the kauri soil and possible environmental drivers. To characterize the functional gene profile in relation to soil microbial diversity of the kauri trees at Auckland Botanic Gardens (ABG), Auckland, New Zealand the GeoChip 5.0 M (Glomics Inc. USA), a microarray-based metagenomics tool, was used. GeoChip 5.0 M comprises of 162,000 probes from 365,000 target genes (coding DNA sequence - CDS), which covers all taxonomic groups (archaea, bacteria, fungi, protists, algae, and viruses) [5]. The ABG has kauri trees that are approximately 20 years old, located in three distinct man-made environments: Native Forest, Kauri Grove, and Rose Garden. We selected two trees from the Native Forest and two from the Kauri Grove for our experiment. Soil samples were collected from the four cardinal points of each tree, at 10 cm depth. Pooled environmental DNA was sent to Glomics (USA) and the data were preprocessed using GeoChip data analysis pipeline described in http://www.ou.edu/ieg/tools/data-analysispipeline.html. Based on the GeoChip data generated from the soil samples, we have detected a total of 946 genes, 4342 taxa, 102 phyla, and 995 genera. The data presented here provide an overview of functional genes associated with kauri soil, which can serve as baseline for other kauri soil microbiome analysis at forest-scale studies. The raw data has been uploaded to Mendeley Data https://doi.org/10.17632/T22NNN385K.1.

Desert and anthropogenic mixing dust deposition influences microbial communities in surface waters of the western Pacific Ocean.

The western Pacific Ocean is particularly affected by dust aerosols due to the transport of desert-natural sand and industrially derived particulate matter with aerodynamic diameter < 2.5 µm (PM2.5) from continental Asia. Both oligotrophic and nutrient-sufficient surface water occurs in this region and these are speculated to support different microbial community dynamics. Here, we report evidence from four shipboard experiments in the western Pacific Ocean supplying oligotrophic and nutrient-sufficient surface waters with aerosol particles obtained from the nearby coastal mountains, to simulate dust and anthropogenic aerosol inputs in the ocean region. A sharp increase in nitrate for surface waters after addition of dust aerosols resulted in large increases in diatom abundance in oligotrophic waters, whilst in nutrient-sufficient waters the response of diatom population was reduced. The increase in organic matter provided by aerosol inputs and/or increase in phytoplankton biomass induced the growth of heterotrophic prokaryotes, such as Rhodobacteraceae and Alteromonadaceae populations, in both oligotrophic and nutrient-sufficient seawater. Anthropogenic and desert-natural dust is an important source of nitrate and organics to oceanic waters and such inputs can directly affect primary production and heterotrophic prokaryotic abundance in the ocean, implying consequences for the carbon cycle in these aerosol-affected waters.

Characterization and Risk Assessment of Atmospheric PM2.5 and PM10 Particulate-Bound PAHs and NPAHs in Rwanda, Central-East Africa.

Exposure to airborne particulates is estimated as the largest cause of premature human mortality worldwide and is of particular concern in sub-Saharan Africa where emissions are high and data are lacking. Particulate matter (PM) contains several toxic organic species including polycyclic aromatic hydrocarbons (PAHs) and nitrated PAHs (NPAHs). This study provides the first characterization and source identification for PM10- and PM2.5-bound PAHs and NPAHs in sub-Saharan Africa during a three-month period that spanned dry and wet seasons at three locations in Rwanda. The 24-h mean PM2.5 and PM10 concentrations were significantly higher in the dry than the wet season. PAH and NPAH concentrations at the urban roadside site were significantly higher than the urban background and rural site. Source identification using diagnostic ratio analysis and principal component analysis (PCA) revealed diesel and gasoline-powered vehicles at the urban location and wood burning at the rural location as the major sources of PAHs and NPAHs. Our analysis demonstrates that PM concentrations and lifetime cancer risks resulting from inhalation exposure to PM-bound PAHs and NPAHs exceed World Health Organization safe limits. This study provides clear evidence that an immediate development of emission control measures is required.

Global Diversity of Desert Hypolithic Cyanobacteria.

Global patterns in diversity were estimated for cyanobacteria-dominated hypolithic communities that colonize ventral surfaces of quartz stones and are common in desert environments. A total of 64 hypolithic communities were recovered from deserts on every continent plus a tropical moisture sufficient location. Community diversity was estimated using a combined t-RFLP fingerprinting and high throughput sequencing approach. The t-RFLP analysis revealed desert communities were different from the single non-desert location. A striking pattern also emerged where Antarctic desert communities were clearly distinct from all other deserts. Some overlap in community similarity occurred for hot, cold and tundra deserts. A further observation was that the producer-consumer ratio displayed a significant negative correlation with growing season, such that shorter growing seasons supported communities with greater abundance of producers, and this pattern was independent of macroclimate. High-throughput sequencing of 16S rRNA and nifH genes from four representative samples validated the t-RFLP study and revealed patterns of taxonomic and putative diazotrophic diversity for desert communities from the Taklimakan Desert, Tibetan Plateau, Canadian Arctic and Antarctic. All communities were dominated by cyanobacteria and among these 21 taxa were potentially endemic to any given desert location. Some others occurred in all but the most extreme hot and polar deserts suggesting they were relatively less well adapted to environmental stress. The t-RFLP and sequencing data revealed the two most abundant cyanobacterial taxa were Phormidium in Antarctic and Tibetan deserts and Chroococcidiopsis in hot and cold deserts. The Arctic tundra displayed a more heterogenous cyanobacterial assemblage and this was attributed to the maritime-influenced sampling location. The most abundant heterotrophic taxa were ubiquitous among samples and belonged to the Acidobacteria, Actinobacteria, Bacteroidetes, and Proteobacteria. Sequencing using nitrogenase gene-specific primers revealed all putative diazotrophs were Proteobacteria of the orders Burkholderiales, Rhizobiales, and Rhodospirillales. We envisage cyanobacterial carbon input to the system is accompanied by nitrogen fixation largely from non-cyanobacterial taxa. Overall the results indicate desert hypoliths worldwide are dominated by cyanobacteria and that growing season is a useful predictor of their abundance. Differences in cyanobacterial taxa encountered may reflect their adaptation to different moisture availability regimes in polar and non-polar deserts.

Multilocus Sequence Analysis of Phylogroup 1 and 2 Oral Treponeme Strains.

More than 75 "species-level" phylotypes of spirochete bacteria belonging to the genus Treponema reside within the human oral cavity. The majority of these oral treponeme phylotypes correspond to as-yet-uncultivated taxa or strains of uncertain standing in taxonomy. Here, we analyze phylogenetic and taxonomic relationships between oral treponeme strains using a multilocus sequence analysis (MLSA) scheme based on the highly conserved 16S rRNA, pyrH, recA, and flaA genes. We utilized this MLSA scheme to analyze genetic data from a curated collection of oral treponeme strains (n = 71) of diverse geographical origins. This comprises phylogroup 1 (n = 23) and phylogroup 2 (n = 48) treponeme strains, including all relevant American Type Culture Collection reference strains. The taxonomy of all strains was confirmed or inferred via the analysis of ca. 1,450-bp 16S rRNA gene sequences using a combination of bioinformatic and phylogenetic approaches. Taxonomic and phylogenetic relationships between the respective treponeme strains were further investigated by analyzing individual and concatenated flaA (1,074-nucleotide [nt]), recA (1,377-nt), and pyrH (696-nt) gene sequence data sets. Our data confirmed the species differentiation between Treponema denticola (n = 41) and Treponema putidum (n = 7) strains. Notably, our results clearly supported the differentiation of the 23 phylogroup 1 treponeme strains into five distinct "species-level" phylotypes. These respectively corresponded to "Treponema vincentii" (n = 11), Treponema medium (n = 1), "Treponema sinensis" (Treponema sp. IA; n = 4), Treponema sp. IB (n = 3), and Treponema sp. IC (n = 4). In conclusion, our MLSA-based approach can be used to effectively discriminate oral treponeme taxa, confirm taxonomic assignment, and enable the delineation of species boundaries with high confidence. IMPORTANCE: Periodontal diseases are caused by persistent polymicrobial biofilm infections of the gums and underlying tooth-supporting structures and have a complex and variable etiology. Although Treponema denticola is strongly associated with periodontal diseases, the etiological roles of other treponeme species/phylotypes are less well defined. This is due to a paucity of formal species descriptions and a poor understanding of genetic relationships between oral treponeme taxa. Our study directly addresses these issues. It represents one of the most comprehensive analyses of oral treponeme strains performed to date, including isolates from North America, Europe, and Asia. We envisage that our results will greatly facilitate future metagenomic efforts aimed at characterizing the clinical distributions of oral treponeme species/phylotypes, helping investigators to establish a more detailed understanding of their etiological roles in periodontal diseases and other infectious diseases. Our results are also directly relevant to various polymicrobial tissue infections in animals, which also involve treponeme populations.

Taxonomic and Functional Diversity of Soil and Hypolithic Microbial Communities in Miers Valley, McMurdo Dry Valleys, Antarctica.

The McMurdo Dry Valleys of Antarctica are an extreme polar desert. Mineral soils support subsurface microbial communities and translucent rocks support development of hypolithic communities on ventral surfaces in soil contact. Despite significant research attention, relatively little is known about taxonomic and functional diversity or their inter-relationships. Here we report a combined diversity and functional interrogation for soil and hypoliths of the Miers Valley in the McMurdo Dry Valleys of Antarctica. The study employed 16S rRNA fingerprinting and high throughput sequencing combined with the GeoChip functional microarray. The soil community was revealed as a highly diverse reservoir of bacterial diversity dominated by actinobacteria. Hypolithic communities were less diverse and dominated by cyanobacteria. Major differences in putative functionality were that soil communities displayed greater diversity in stress tolerance and recalcitrant substrate utilization pathways, whilst hypolithic communities supported greater diversity of nutrient limitation adaptation pathways. A relatively high level of functional redundancy in both soil and hypoliths may indicate adaptation of these communities to fluctuating environmental conditions.

Niche Filtering of Bacteria in Soil and Rock Habitats of the Colorado Plateau Desert, Utah, USA.

A common feature of microbial colonization in deserts is biological soil crusts (BSCs), and these comprise a complex community dominated by Cyanobacteria. Rock substrates, particularly sandstone, are also colonized by microbial communities. These are separated by bare sandy soil that also supports microbial colonization. Here we report a high-throughput sequencing study of BSC and cryptoendolith plus adjacent bare soil communities in the Colorado Plateau Desert, Utah, USA. Bare soils supported a community with low levels of recoverable DNA and high evenness, whilst BSC yielded relatively high recoverable DNA, and reduced evenness compared to bare soil due to specialized crust taxa. The cryptoendolithic community displayed the greatest evenness but the lowest diversity, reflecting the highly specialized nature of these communities. A strong substrate-dependent pattern of community assembly was observed, and in particular cyanobacterial taxa were distinct. Soils were virtually devoid of photoautotrophic signatures, BSC was dominated by a closely related group of Microcoleus/Phormidium taxa, whilst cryptoendolithic colonization in sandstone supported almost exclusively a single genus, Chroococcidiopsis. We interpret this as strong evidence for niche filtering of taxa in communities. Local inter-niche recruitment of photoautotrophs may therefore be limited and so communities likely depend significantly on cyanobacterial recruitment from distant sources of similar substrate. We discuss the implication of this finding in terms of conservation and management of desert microbiota.

Radiation-Tolerant Bacteria Isolated from High Altitude Soil in Tibet.

This study reports the identification of ionising radiation tolerant bacteria from a high elevation arid region of central Tibet. Nineteen isolates were isolated from soil exposed to ionising radiation at doses from 0 to 15 kGy. Isolates were phylogenetically characterised using 16S rRNA gene sequences. Most isolates comprised taxa from the Actinobacteria, Cyanobacteria, Firmicutes and proteobacteria and these survived doses up to 5 kGy. The Firmicutes and Deinococci also survived doses up to 10 kGy, and the highest dose of 15 kGy was survived only by the Deinococci. No altitude-related pattern was discernible within the range 4638-5240 m, instead culturable bacterial estimates for irradiated soil were strongly influenced by the abundance of Deinococci. We conclude that the relatively high UV exposure in Tibet has contributed to the high diversity of radiation tolerant soil bacteria. In addition, the strong association between desiccation-tolerance and radiation tolerance pathways suggests the arid environment may also have selected in favour of radiation tolerant taxa.

Distributions of Synergistetes in clinically-healthy and diseased periodontal and peri-implant niches.

Bacterial taxa belonging to the phylum Synergistetes are commonly detected within diseased periodontal niches, but are rarely found within healthy oral sites. However, as they typically constitute a minor fraction of the oral microbiota, their precise distributions and disease-associations remain to be fully established. Here, we surveyed the Synergistetes taxa present within individual periodontal/subgingival and peri-implant/submucosal sites, within Chinese subjects (n = 18) affected by both peri-implantitis and periodontitis. Four individual, clinically-distinct sites were analyzed in each patient: healthy sulcus; periodontitis lesion; healthy peri-implant space; peri-implantitis lesion. We employed a clone library-based approach, using PCR-primers that specifically amplified ca. 650bp regions of the 16S rRNA gene from oral cluster A and B Synergistetes taxa. Twenty-one of the 72 sites (from 12/18 subjects) yielded Synergistetes 16S rRNA PCR products. Sequencing of cloned amplicon libraries yielded 1338 quality-filtered 16S rRNA sequences, which were assigned to 26 Synergistetes operational taxonomic units (OTUs; oral taxon SH01-SH26) using a 98.5% identity cut-off. We identified 25 Synergistetes oral cluster A OTUs (genus Fretibacterium; corresponding to Human Oral Taxon (HOT) numbers 358, 359, 360, 361, 362, 363, 452, and 453), and one oral cluster B OTU (Pyramidobacter piscolens oral taxon SH04, HOT-357). Three OTUs predominated: Fretibacterium oral taxon SH01 (HOT-360), Fretibacterium oral taxon SH02 (HOT-452), and Fretibacterium fastidiosum oral taxon SH03 (HOT-363). The Synergistetes community compositions within the respective periodontal and peri-implant sites were variable and complex, and no statistically-significant correlations could be established. However, the detection frequency of F. fastidiosum SH03 and Fretibacterium oral taxon SH01 were both positively associated with plaque index at healthy subgingival sites. Taken together, our results show that diverse Synergistetes populations inhabit both diseased and healthy periodontal and peri-implant niches, with considerable site-to-site variations in composition occurring within the same oral cavity.

In-depth snapshot of the equine subgingival microbiome.

This study explored the range of bacterial taxa present within healthy subgingival (below the gum-line) niches in the horse oral cavity using 16S rRNA gene amplicon pyrosequencing. Pooled subgingival plaque samples were collected from approximately 200 sulcus sites from two horses (EQ1, EQ2) for analysis. A total of 14,260 quality-filtered pyrosequencing reads were obtained, which were assigned to 3875 operational taxonomic units (OTUs; 99% identity cut-off); 1907 OTUs for EQ1 and 2156 OTUs for EQ2. Diverse taxa from 12 phyla were identified, including Actinobacteria (3.17%), Bacteroidetes (25.11%), Chloroflexi (0.04%), Firmicutes (27.57%), Fusobacteria (5.15%), Proteobacteria (37.67%), Spirochaetes (0.15%), Synergistetes (0.22%), Tenericutes (0.16%), GN02 (0.19%), SR1 (0.01%) and TM7 (0.37%). Many OTUs were not closely related to known phylotypes, and may represent 'equine-specific' taxa. Phylotypes corresponding to Gammaproteobacteria were abundant, including Actinobacillus spp. (8.75%), unclassified Pasteurellaceae (9.90%) and Moraxella spp. (9.58%). PCR targeting the Synergistetes and Spirochaetes phyla was performed, and resultant plasmid libraries of 16S rRNA gene amplicons (ca. 1480 bp) were Sanger sequenced. Twenty-six Spirochaetes OTUs, and 16 Synergistetes OTUs were identified (99% identity cut-off). These 'species-level' OTUs were assigned Equine Oral Taxon (EOT) numbers, whose phylogenies and taxonomy were comprehensively investigated, in conjunction with corresponding Synergistetes and Spirochaetes OTUs identified by pyrosequencing. The vast majority of Spirochaetes taxa belonged to the genus Treponema, which corresponded to 7 of the 10 human oral treponeme phylogroups. Other Spirochaetes taxa belonging to the Leptospiraceae family were observed; but many treponemes commonly implicated in animal hoof/foot and non-oral soft tissue infections; e.g. Treponema phagedenis, Treponema pedis, Treponema refringens, Treponema calligyrum; were not identified here. Diverse Synergistetes taxa corresponding to oral clusters A and B were identified, which included Fretibacterium fastidiosum and Pyramidobacter piscolens. Taken together, our data reveals that equine subgingival plaque microbiota shares many similarities with the human, canine and feline oral microbiomes.

Complete Genome Sequence for Treponema sp. OMZ 838 (ATCC 700772, DSM 16789), Isolated from a Necrotizing Ulcerative Gingivitis Lesion.

The oral treponeme bacterium Treponema sp. OMZ 838 was originally isolated from a human necrotizing ulcerative gingivitis (NUG) lesion. Its taxonomic status remains uncertain. The complete genome sequence length was determined to be 2,708,067 bp, with a G+C content of 44.58%, and 2,236 predicted coding DNA sequences (CDS).

Complete Genome Sequence of the Oral Spirochete Bacterium Treponema putidum Strain OMZ 758T (ATCC 700334T).

The oral spirochete bacterium Treponema putidum inhabits human periodontal niches. The complete genome sequence of the OMZ 758(T) (ATCC 700334(T)) strain of this species was determined, revealing a 2,796,913-bp chromosome, with a G+C content of 37.30% and a single plasmid (pTPu1; 3,649 bp) identical to pTS1 from Treponema denticola.

pZMO7-Derived shuttle vectors for heterologous protein expression and proteomic applications in the ethanol-producing bacterium Zymomonas mobilis.

BACKGROUND: The ethanol-producing bacterium Zymomonas mobilis has attracted considerable scientific and commercial interest due to its exceptional physiological properties. Shuttle vectors derived from native plasmids have previously been successfully used for heterologous gene expression in this bacterium for a variety of purposes, most notably for metabolic engineering applications. RESULTS: A quantitative PCR (qPCR) approach was used to determine the copy numbers of two endogenous double stranded DNA plasmids: pZMO1A (1,647 bp) and pZMO7 (pZA1003; 4,551 bp) within the NCIMB 11163 strain of Z. mobilis. Data indicated pZMO1A and pZMO7 were present at ca. 3-5 and ca. 1-2 copies per cell, respectively. A ca. 1,900 bp fragment from plasmid pZMO7 was used to construct two Escherichia coli - Z. mobilis shuttle vectors (pZ7C and pZ7-184). The intracellular stabilities and copy numbers of pZ7C and pZ7-184 were characterized within the NCIMB 11163, ATCC 29191 and (ATCC 10988-derived) CU1 Rif2 strains of Z. mobilis. Both shuttle vectors could be stably maintained within the ATCC 29191 strain (ca. 20-40 copies per cell), and the CU1 Rif2 strain (ca. 2-3 copies per cell), for more than 50 generations in the absence of an antibiotic selectable marker. A selectable marker was required for shuttle vector maintenance in the parental NCIMB 11163 strain; most probably due to competition for replication with the endogenous pZMO7 plasmid molecules. N-terminal glutathione S-transferase (GST)-fusions of four endogenous proteins, namely the acyl-carrier protein (AcpP); 2-dehydro-3-deoxyphosphooctonate aldolase (KdsA); DNA polymerase III chi subunit (HolC); and the RNA chaperone protein Hfq; were successfully expressed from pZ7C-derived shuttle vectors, and their protein-protein binding interactions were analyzed in Z. mobilis ATCC 29191. Using this approach, proteins that co-purified with AcpP and KdsA were identified. CONCLUSIONS: We show that a shuttle vector-based protein affinity 'pull-down' approach can be used to probe protein interaction networks in Z. mobilis cells. Our results demonstrate that protein expression plasmids derived from pZMO7 have significant potential for use in future biological or biotechnological applications within Z. mobilis.

Multilocus sequence analysis of Treponema denticola strains of diverse origin.

BACKGROUND: The oral spirochete bacterium Treponema denticola is associated with both the incidence and severity of periodontal disease. Although the biological or phenotypic properties of a significant number of T. denticola isolates have been reported in the literature, their genetic diversity or phylogeny has never been systematically investigated. Here, we describe a multilocus sequence analysis (MLSA) of 20 of the most highly studied reference strains and clinical isolates of T. denticola; which were originally isolated from subgingival plaque samples taken from subjects from China, Japan, the Netherlands, Canada and the USA. RESULTS: The sequences of the 16S ribosomal RNA gene, and 7 conserved protein-encoding genes (flaA, recA, pyrH, ppnK, dnaN, era and radC) were successfully determined for each strain. Sequence data was analyzed using a variety of bioinformatic and phylogenetic software tools. We found no evidence of positive selection or DNA recombination within the protein-encoding genes, where levels of intraspecific sequence polymorphism varied from 18.8% (flaA) to 8.9% (dnaN). Phylogenetic analysis of the concatenated protein-encoding gene sequence data (ca. 6,513 nucleotides for each strain) using Bayesian and maximum likelihood approaches indicated that the T. denticola strains were monophyletic, and formed 6 well-defined clades. All analyzed T. denticola strains appeared to have a genetic origin distinct from that of 'Treponema vincentii' or Treponema pallidum. No specific geographical relationships could be established; but several strains isolated from different continents appear to be closely related at the genetic level. CONCLUSIONS: Our analyses indicate that previous biological and biophysical investigations have predominantly focused on a subset of T. denticola strains with a relatively narrow range of genetic diversity. Our methodology and results establish a genetic framework for the discrimination and phylogenetic analysis of T. denticola isolates, which will greatly assist future biological and epidemiological investigations involving this putative 'periodontopathogen'.