Draft Genome Sequence of the Versatile Alkane-Degrading Bacterium Aquabacterium sp. Strain NJ1

Native freshwater lake microbial community response to an in situ experimental dilbit spill

With the increase in crude oil transport throughout Canada, the potential for spills into freshwater ecosystems has increased and additional research is needed in these sensitive environments. Large enclosures erected in a lake were used as mesocosms for this controlled experimental dilbit (diluted bitumen) spill under ambient environmental conditions. The microbial response to dilbit, the efficacy of standard remediation protocols on different shoreline types commonly found in Canadian freshwater lakes, including a testing of a shoreline washing agent were all evaluated. We found that the native microbial community did not undergo any significant shifts in composition after exposure to dilbit or the ensuing remediation treatments. Regardless of the treatment, sample type (soil, sediment, or water), or type of associated shoreline, the community remained relatively consistent over a 3-month monitoring period. Following this, metagenomic analysis of polycyclic aromatic and alkane hydrocarbon degradation mechanisms also showed that while many key genes identified in PAH and alkane biodegradation were present, their abundance did not change significantly over the course of the experiment. These results showed that the native microbial community present in a pristine freshwater lake has the prerequisite mechanisms for hydrocarbon degradation in place, and combined with standard remediation practices in use in Canada, has the genetic potential and resilience to potentially undertake bioremediation.

Holobiont Urbanism: sampling urban beehives reveals cities' metagenomes

BACKGROUND

Over half of the world's population lives in urban areas with, according to the United Nations, nearly 70% expected to live in cities by 2050. Our cities are built by and for humans, but are also complex, adaptive biological systems involving a diversity of other living species. The majority of these species are invisible and constitute the city's microbiome. Our design decisions for the built environment shape these invisible populations, and as inhabitants we interact with them on a constant basis. A growing body of evidence shows us that human health and well-being are dependent on these interactions. Indeed, multicellular organisms owe meaningful aspects of their development and phenotype to interactions with the microorganisms-bacteria or fungi-with which they live in continual exchange and symbiosis. Therefore, it is meaningful to establish microbial maps of the cities we inhabit. While the processing and sequencing of environmental microbiome samples can be high-throughput, gathering samples is still labor and time intensive, and can require mobilizing large numbers of volunteers to get a snapshot of the microbial landscape of a city.

RESULTS

Here we postulate that honeybees may be effective collaborators in gathering samples of urban microbiota, as they forage daily within a 2-mile radius of their hive. We describe the results of a pilot study conducted with three rooftop beehives in Brooklyn, NY, where we evaluated the potential of various hive materials (honey, debris, hive swabs, bee bodies) to reveal information as to the surrounding metagenomic landscape, and where we conclude that the bee debris are the richest substrate. Based on these results, we profiled 4 additional cities through collected hive debris: Sydney, Melbourne, Venice and Tokyo. We show that each city displays a unique metagenomic profile as seen by honeybees. These profiles yield information relevant to hive health such as known bee symbionts and pathogens. Additionally, we show that this method can be used for human pathogen surveillance, with a proof-of-concept example in which we recover the majority of virulence factor genes for Rickettsia felis, a pathogen known to be responsible for "cat scratch fever".

CONCLUSIONS

We show that this method yields information relevant to hive health and human health, providing a strategy to monitor environmental microbiomes on a city scale. Here we present the results of this study, and discuss them in terms of architectural implications, as well as the potential of this method for epidemic surveillance.

Succession Patterns of Microbial Composition and Activity following the Diesel Spill in an Urban River

Diesel spills in freshwater systems have adverse impacts on the water quality and the shore wetland. Microbial degradation is the major and ultimate natural mechanism that can clean the diesel from the environment. However, which, and how fast, diesel-degrading microorganisms could degrade spilled diesel has not been well-documented in river water. Using a combination of 14C-/3H--based radiotracer assays, analytical chemistry, MiSeq sequencing, and simulation-based microcosm incubation approaches, we demonstrated succession patterns of microbial diesel-degrading activities, and bacterial and fungal community compositions. The biodegradation activities of alkanes and polycyclic aromatic hydrocarbons (PAHs) were induced within 24 h after diesel addition, and reached their maximum after incubation for 7 days. Potential diesel-degrading bacteria Perlucidibaca, Acinetobacter, Pseudomonas, Acidovorax, and Aquabacterium dominated the community initially (day 3 and day 7), but later community structure (day 21) was dominated by bacteria Ralstonia and Planctomyces. The key early fungi responders were Aspergillus, Mortierella, and Phaeoacremonium by day 7, whereas Bullera and Basidiobolus dominated the fungal community at day 21. These results directly characterize the rapid response of microbial community to diesel spills, and suggest that the progression of diesel microbial degradation is performed by the cooperative system of the versatile obligate diesel-degrading and some general heterotrophic microorganisms in river diesel spills.

Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand

Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.

Specific enrichment of hydrocarbonclastic bacteria from diesel-amended soil on biochar particles

Biochar has been proposed as a suitable biostimulant for the remediation of hydrocarbon contamination, and also has the potential to act as a carrier for hydrocarbonoclastic microorganisms which could bioaugment endogenous microbial communities. However, the evidence regarding the biostimulatory effects of biochars on hydrocarbon bioremediation is somewhat equivocal, possibly due to variability of the physicochemical properties of biochar and soil across studies. Here, we use standard biochars with defined properties produced from softwood pellets (SWP) and rice husk (RH) at pyrolysis temperatures of 550 °C or 700 °C to test the effects of biochar amendment on microbial community composition and hydrocarbon degradation in soil microcosms contaminated with diesel oil. Combining this approach for the first time with specific analysis of microbial community composition using amplicon sequence variants (ASVs), we find that oil contamination causes extreme short-term loss of soil microbial diversity, and highly-specific selection of a limited set of genera defined by 13 ASVs. Biochar ameliorates the short-term loss of diversity, and in the longer term (9 weeks), changes community composition in a type-specific manner. The majority of the 13 selected ASVs are further enriched on biochar particles, although SWP biochars perform better than RH biochar in enrichment of putative hydrocarbonoclastic Aquabacterium spp. However, complete degradation of normal (n) alkanes from the aliphatic hydrocarbon fraction is prevented in the presence of biochar amendment, possibly due to their adsorption onto the char surface. Furthermore, we show that putative hydrocarbon degraders released from diesel-amended soil can subsequently be enriched to high levels on SWP biochar particles in growth medium supplemented with diesel oil as the sole carbon source; these include selected ASVs representing the genera Rhodococcus, Aquabacterium, and Cavicella. This work suggests that use of biochar pre-enriched with endogenous, conditionally-rare hydrocarbon degrading bacteria is a promising strategy for bioaugmentation of diesel-contaminated soils.

Linking microbial community composition to hydrogeochemistry in the western Hetao Basin: Potential importance of ammonium as an electron donor during arsenic mobilization

Various functional groups of microorganisms and related biogeochemical processes are likely to control arsenic (As) mobilization in groundwater systems. However, spatially-dependent correlations between microbial community composition and geochemical zonation along groundwater flow paths are not fully understood, especially with respect to arsenic mobility. The western Hetao Basin was selected as the study area to address this limitation, where groundwater flows from a proximal fan (geochemical-group I: low As, oxidizing), through a transition area (geochemical-group II: moderate As, moderately-reducing) and then to a flat plain (geochemical-group III: high As, reducing). High-throughput Illumina 16S rRNA gene sequencing showed that the microbial community structure in the proximal fan included bacteria affiliated with organic carbon degradation and nitrate-reduction or even nitrate-dependant Fe(II)-oxidation, mainly resulting in As immobilization. In contrast, for the flat plain, high As groundwater contained Fe(III)- and As(V)-reducing bacteria, consistent with current models on As mobilization driven via reductive dissolution of Fe(III)/As(V) mineral assemblages. However, Spearman correlations between hydrogeochemical data and microbial community compositions indicated that ammonium as a possible electron donor induced reduction of Fe oxide minerals, suggesting a wider range of metabolic pathways (including ammonium oxidation coupled with Fe(III) reduction) driving As mobilization in high As groundwater systems.

Does Quorum Sensing play a role in microbial shifts along spontaneous fermentation of cocoa beans? An in silico perspective

Cocoa fermentation is a spontaneous process shaped by a variable microbial ecosystem which is assembled due to cross-feeding relationship among yeasts and bacteria, resulting in a synchronized microbial succession started by yeasts, followed by lactic acid bacteria (LAB) and finalized by acetic acid bacteria (AAB). Several studies have indicated the effect of microbial interactions in food ecosystems highlighting the importance of quorum sensing (QS) in bacterial adaptation in harsh environments modulating several phenotypes such as biofilm formation, tolerance to acid stress, bacteriocin production, competence, morphological modifications, motility, among others. However, antagonic interactions also occur, and can be marked by Quorum Quenching (QQ) activity, negatively impacting QS regulated phenotypes. Our current knowledge regarding microbial cocoa composition and functioning is based on culture-based analysis and culture-independent PCR-based methods. Therefore, we set out to investigate the application of metagenomics analysis on a classical spontaneous cocoa fermentation in order to describe: (I) the microbial taxonomic composition; (II) the functional potential of the cocoa microbiome; (III) the microbiome putative QS potential; and (IV) the microbiome QQ potential. Both aims III and IV are related to the expression of effectors that may confer advantageous traits along fermentation which can explain their dominance in specific time zones during the entire process. We have observed a bacterial succession shaped by yeasts and filamentous fungi and then Enterobacteriaceales, LAB and AAB, as well as a diverse genetic metabolic potential related to proteins and carbohydrates metabolism associated to the yeast Saccharomyces cerevisiae and members of the Enterobacteriaceales order and LAB and AAB groups. In addition, in silico evidences of interspecific QS arsenal were found in members of the genera Enterobacter, Lactobacillus, Bacillus and Pantoea, while inferences of intraspecific QS potential were found in the members of the genera Bacillus, Enterobacter, Komagataeibacter, Lactobacillus and Pantoea. In addition, a QQ potential was detected in Lactobacillus and in AAB members. These findings indicate that QS and QQ may modulate bacterial dominance in different time points during fermentation, along with cross-feeding, being responsible for their maintenance in a large time range.

Succession Patterns and Physical Niche Partitioning in Microbial Communities from Subsurface Coal Seams

The subsurface represents a largely unexplored frontier in microbiology. Here, coal seams present something of an oasis for microbial life, providing moisture, warmth, and abundant fossilized organic material. Microbes in coal seams are thought to syntrophically mobilize fossilized carbon from the geosphere to the biosphere. Despite the environmental and economic importance of this process, little is known about the microbial ecology of coal seams. In the current study, ecological succession and spatial niche partitioning are explored in three coal seam microbial communities. Scanning electron microscopic visualization and 16S rRNA sequencing track changes in microbial communities over time, revealing distinct attached and planktonic communities displaying patterns of ecological succession. Attachment to the coal surface is biofilm mediated on Surat coal, whereas microbes on Sydney and Gunnedah coal show different attachment processes. This study demonstrates that coal seam microbial communities undergo spatial niche partitioning during periods of succession as microbes colonize coal environments.

•

Coal surfaces and waters have distinctly different microbial communities

•

Microbes attach to coal surfaces via multiple adhesion strategies

•

Adhesion strategies include biofilm formation and direct cell attachment

•

Coal microbe succession patterns provide insights into possible community roles

Bioprospecting for microbes with potential hydrocarbon remediation activity on the northwest coast of the Yucatan Peninsula, Mexico, using DNA sequencing

Coastal environments harbor diverse microbial communities, which can contain genera with potential bioremediation activity. Next-generation DNA sequencing was used to identify bacteria to the genus level in water and sediment samples collected from the open ocean, shoreline, wetlands and freshwater upwellings on the northwest coast of the Yucatan Peninsula. Supported by an extensive literature review, a phylogenetic investigation of the communities was done using reconstruction of unobserved states software (PICRUSt) to predict metagenome functional content from the sequenced 16S gene in all the samples. Bacterial genera were identified for their potential hydrocarbon bioremediation activity. These included generalist genera commonly reported in hydrocarbon-polluted areas and petroleum reservoirs, as well as specialists such as Alcanivorax and Cycloclasticus. The highest readings for bacteria with potential hydrocarbon bioremediation activity were for the genera Vibrio, Alteromonas, Pseudomonas, Acinetobacter, Burkholderia, Acidovorax and Pseudoalteromonas from different environments in the study area. Some genera were identified only in specific sites; for example, Aquabacterium and Polaromonas were found only in freshwater upwellings. Variation in genera distribution was probably due to differences in environmental conditions in the sampled zones. Bacterial diversity was high in the study area and included numerous genera with known bioremediation activity. Functional prediction of the metagenome indicated that the studied bacterial communities would most probably degrade toluene, naphthalene, chloroalkane and chloroalkene, with lower degradation proportions for aromatic hydrocarbons, fluorobenzoate and xylene. Differences in predicted degradation existed between sediments and water, and between different locations.

Evaluation of an up-flow anaerobic sludge bed (UASB) reactor containing diatomite and maifanite for the improved treatment of petroleum wastewater

Novel diatomite (R1) and maifanite (R2) were utilized as support materials in an up-flow anaerobic sludge bed (UASB) reactor for the treatment of recalcitrant petroleum wastewater. At high organic loadings (11kg-COD/m³·d), these materials were efficient at reducing COD (92.7% and 93.0%) in comparison with controls (R0) (88.4%). Higher percentages of large granular sludge (0.6mm or larger) were observed for R1 (30.3%) and R2 (24.6%) compared with controls (22.6%). The larger portion of granular sludge provided a favorable habitat that resulted in greater microorganism diversity. Increased filamentous bacterial communities are believed to have promoted granular sludge formation promoting a conductive environment for stimulation methanogenic Archaea. These communities had enhanced pH tolerance and produced more methane. This study illustrates a new potential use of diatomite and maifanite as support materials in UASB reactors for increased efficiency when treating refractory wastewaters.

Novel arsenic-transforming bacteria and the diversity of their arsenic-related genes and enzymes arising from arsenic-polluted freshwater sediment

Bacteria are essential in arsenic cycling. However, few studies have addressed 16S rRNA and arsenic-related functional gene diversity in long-term arsenic-contaminated tropical sediment. Here, using culture-based, metagenomic and computational approaches, we describe the diversity of bacteria, genes and enzymes involved in AsIII and AsV transformation in freshwater sediment and in anaerobic AsIII- and AsV-enrichment cultures (ECs). The taxonomic profile reveals significant differences among the communities. Arcobacter, Dechloromonas, Sedimentibacter and Clostridium thermopalmarium were exclusively found in ECs, whereas Anaerobacillus was restricted to AsV-EC. Novel taxa that are both AsV-reducers and AsIII-oxidizers were identified: Dechloromonas, Acidovorax facilis, A. delafieldii, Aquabacterium, Shewanella, C. thermopalmarium and Macellibacteroides fermentans. Phylogenic discrepancies were revealed among the aioA, arsC and arrA genes and those of other species, indicating horizontal gene transfer. ArsC and AioA have sets of amino acids that can be used to assess their functional and structural integrity and familial subgroups. The positions required for AsV reduction are conserved, suggesting strong selective pressure for maintaining the functionality of ArsC. Altogether, these findings highlight the role of freshwater sediment bacteria in arsenic mobility, and the untapped diversity of dissimilatory arsenate-reducing and arsenate-resistant bacteria, which might contribute to arsenic toxicity in aquatic environments.

Temporal dynamics of microbial communities in microcosms in response to pollutants

Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n-octadecane, phenanthrene + n-octadecane and phenanthrene + n-octadecane + CdCl₂ ). Subculturing was performed at 10-day intervals, followed by high-throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co-occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re-equilibration of microbial communities.

Occurrence of diverse alkane hydroxylase alkB genes in indigenous oil-degrading bacteria of Baltic Sea surface water

Formation of specific oil degrading bacterial communities in diesel fuel, crude oil, heptane and hexadecane supplemented microcosms of the Baltic Sea surface water samples was revealed. The 475 sequences from constructed alkane hydroxylase alkB gene clone libraries were grouped into 30 OPFs. The two largest groups were most similar to Pedobacter sp. (245 from 475) and Limnobacter sp. (112 from 475) alkB gene sequences. From 56 alkane-degrading bacterial strains 41 belonged to the Pseudomonas spp. and 8 to the Rhodococcus spp. having redundant alkB genes. Together 68 alkB gene sequences were identified. These genes grouped into 20 OPFs, half of them being specific only to the isolated strains. Altogether 543 diverse alkB genes were characterized in the brackish Baltic Sea water; some of them representing novel lineages having very low sequence identities with corresponding genes of the reference strains.