A comparison of methods for total community DNA preservation and extraction from various thermal environments

The telencephalon is a neuronal substrate for systemic inflammatory responses in teleosts via polyamine metabolism

Systemic inflammation elicits sickness behaviors and fever by engaging a complex neuronal circuitry that begins in the preoptic area of the hypothalamus. Ectotherms such as teleost fish display sickness behaviors in response to infection or inflammation, seeking warmer temperatures to enhance survival via behavioral fever responses. To date, the hypothalamus is the only brain region implicated in sickness behaviors and behavioral fever in teleosts. Yet, the complexity of neurobehavioral manifestations underlying sickness responses in teleosts suggests engagement of higher processing areas of the brain. Using in vivo models of systemic inflammation in rainbow trout, we find canonical pyrogenic cytokine responses in the hypothalamus whereas in the telencephalon and the optic tectum il-1b and tnfa expression is decoupled from il-6 expression. Polyamine metabolism changes, characterized by accumulation of putrescine and decreases in spermine and spermidine, are recorded in the telencephalon but not hypothalamus upon systemic injection of bacteria. While systemic inflammation causes canonical behavioral fever in trout, blockade of bacterial polyamine metabolism prior to injection abrogates behavioral fever, polyamine responses, and telencephalic but not hypothalamic cytokine responses. Combined, our work identifies the telencephalon as a neuronal substrate for brain responses to systemic inflammation in teleosts and uncovers the role of polyamines as critical chemical mediators in sickness behaviors.

A brain microbiome in salmonids at homeostasis

Ectotherms have peculiar relationships with microorganisms. For instance, bacteria are recovered from the blood and internal organs of healthy teleosts. However, the presence of microbial communities in the healthy teleost brain has not been proposed. Here, we report a living bacterial community in the brain of healthy salmonids with bacterial loads comparable to those of the spleen and 1000-fold lower than in the gut. Brain bacterial communities share >50% of their diversity with gut and blood bacterial communities. Using culturomics, we obtained 54 bacterial isolates from the brains of healthy trout. Comparative genomics suggests that brain bacteria may have adaptations for niche colonization and polyamine biosynthesis. In a natural system, Chinook salmon brain microbiomes shift from juveniles to reproductively mature adults. Our study redefines the physiological relationships between the brain and bacteria in teleosts. This symbiosis may endow salmonids with a direct mechanism to sense and respond to environmental microbes.

Sex-dependent effects of mechanical delousing on the skin microbiome of broodstock Atlantic salmon (Salmo salar L.)

Delousing strategies, including mechanical delousing, are typically used to treat Atlantic salmon (Salmo salar) sea lice infestations. In this study, we evaluate the impact of mechanical delousing (Hydrolicer) on the skin bacterial microbiome of broodstock female and male Atlantic salmon. 16S rDNA sequencing of salmon skin microbial communities was performed immediately before delousing, right after delousing and 2 and 13 days post-delousing (dpd). The skin bacterial community of female salmon was more diverse than that of males at the start of the experiment. Overall, hydrolycer caused losses in alpha diversity in females and increases in alpha diversity in males. Hydrolicer also caused rapid shifts in the skin microbial community composition immediately after delicing in a sex-specific manner. There was a decrease in abundance of Proteobacteria and Bacteriodetes in both female and male salmon, whereas Firmicutes and Tenericutes abundances increased. Interestingly, the female community recovered faster, while the male community remained dysbiotic 13 dpd due to expansions in Bacteroidetes (Pseudomonadaceae) and Firmicutes. Our data suggest that female broodstock are more resilient to Hydrolicer treatment due to their more diverse skin microbiota community, and that sex influences the skin microbial community and therefore host health outcomes during common farming manipulations.

Secretory IgM (sIgM) is an ancient master regulator of microbiota homeostasis and metabolism

The co-evolution between secretory immunoglobulins (sIgs) and microbiota began with the emergence of IgM over half a billion years ago. Yet, IgM function in vertebrates is mostly associated with systemic immunity against pathogens. sIgA and sIgT are the only sIgs known to be required in the control of microbiota homeostasis in warm- and cold-blooded vertebrates respectively. Recent studies have shown that sIgM coats a large proportion of the gut microbiota of humans and teleost fish, thus suggesting an ancient and conserved relationship between sIgM and microbiota early in vertebrate evolution. To test this hypothesis, we temporarily and selectively depleted IgM from rainbow trout, an old bony fish species. IgM depletion resulted in a drastic reduction in microbiota IgM coating levels and losses in gutassociated bacteria. These were accompanied by bacterial translocation, severe gut tissue damage, inflammation and dysbiosis predictive of metabolic shifts. Furthermore, depletion of IgM resulted in body weight loss and lethality in an experimental colitis model. Recovery of sIgM to physiological levels restores tissue barrier integrity, while microbiome homeostasis and their predictive metabolic capabilities are not fully restituted. Our findings uncover a previously unrecognized role of sIgM as an ancient master regulator of microbiota homeostasis and metabolism and challenge the current paradigm that sIgA and sIgT are the key vertebrate sIgs regulating microbiome homeostasis.

ONE-SENTENCE SUMMARY

IgM, the most ancient and conserved immunoglobulin in jawed vertebrates, is required for successful symbiosis with the gut microbiota.

Capturing marine microbiomes and environmental DNA: A field sampling guide

The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection and preservation standard practices to enable comparative assessments of results across studies and facilitate meta-analyses. We support this effort by providing guidelines based on a review of published methods and field sampling experiences. The major components considered here are environmental and resource considerations, sample processing strategies, sample storage options, and eDNA extraction protocols. It is impossible to provide universal recommendations considering the wide range of eDNA applications; rather, we provide information to design fit-for-purpose protocols. To manage scope, the focus here is on sampling collection and preservation of prokaryotic and microeukaryotic eDNA. Even with a focused view, the practical utility of any approach depends on multiple factors, including habitat type, available resources, and experimental goals. We broadly recommend enacting rigorous decontamination protocols, pilot studies to guide the filtration volume needed to characterize the target(s) of interest and minimize PCR inhibitor collection, and prioritizing sample freezing over (only) the addition of preservation buffer. An annotated list of studies that test these parameters is included for more detailed investigation on specific steps. To illustrate an approach that demonstrates fit-for-purpose methodologies, we provide a protocol for eDNA sampling aboard an oceanographic vessel. These guidelines can aid the decision-making process for scientists interested in sampling and sequencing marine microbiomes and/or eDNA.

Limits to the three domains of life: lessons from community assembly along an Antarctic salinity gradient

Extremophiles exist among all three domains of life; however, physiological mechanisms for surviving harsh environmental conditions differ among Bacteria, Archaea and Eukarya. Consequently, we expect that domain-specific variation of diversity and community assembly patterns exist along environmental gradients in extreme environments. We investigated inter-domain community compositional differences along a high-elevation salinity gradient in the McMurdo Dry Valleys, Antarctica. Conductivity for 24 soil samples collected along the gradient ranged widely from 50 to 8355 µS cm-1. Taxonomic richness varied among domains, with a total of 359 bacterial, 2 archaeal, 56 fungal, and 69 non-fungal eukaryotic operational taxonomic units (OTUs). Richness for bacteria, archaea, fungi, and non-fungal eukaryotes declined with increasing conductivity (all P < 0.05). Principal coordinate ordination analysis (PCoA) revealed significant (ANOSIM R = 0.97) groupings of low/high salinity bacterial OTUs, while OTUs from other domains were not significantly clustered. Bacterial beta diversity was unimodally distributed along the gradient and had a nested structure driven by species losses, whereas in fungi and non-fungal eukaryotes beta diversity declined monotonically without strong evidence of nestedness. Thus, while increased salinity acts as a stressor in all domains, the mechanisms driving community assembly along the gradient differ substantially between the domains.

The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain

Marine sediments harbor an outstanding level of microbial diversity supporting diverse metabolic activities. Sediments in the Gulf of Mexico (GoM) are subjected to anthropic stressors including oil pollution with potential effects on microbial community structure and function that impact biogeochemical cycling. We used metagenomic analyses to provide significant insight into the potential metabolic capacity of the microbial community in Southern GoM deep sediments. We identified genes for hydrocarbon, nitrogen and sulfur metabolism mostly affiliated with Alpha and Betaproteobacteria, Acidobacteria, Chloroflexi and Firmicutes, in relation to the use of alternative carbon and energy sources to thrive under limiting growth conditions, and metabolic strategies to cope with environmental stressors. In addition, results show amino acids metabolism could be associated with sulfur metabolism carried out by Acidobacteria, Chloroflexi and Firmicutes, and may play a crucial role as a central carbon source to favor bacterial growth. We identified the tricarboxylic acid cycle (TCA) and aspartate, glutamate, glyoxylate and leucine degradation pathways, as part of the core carbon metabolism across samples. Further, microbial communities from the continental slope and abyssal plain show differential metabolic capacities to cope with environmental stressors such as oxidative stress and carbon limiting growth conditions, respectively. This research combined taxonomic and functional information of the microbial community from Southern GoM sediments to provide fundamental knowledge that links the prokaryotic structure to its potential function and which can be used as a baseline for future studies to model microbial community responses to environmental perturbations, as well as to develop more accurate mitigation and conservation strategies.

The lungfish cocoon is a living tissue with antimicrobial functions

Terrestrialization is an extreme physiological adaptation by which African lungfish survive dry seasons. For months and up to several years, lungfish live inside a dry mucus cocoon that protects them from desiccation. Light and electron microscopy reveal that the lungfish cocoon is a living tissue that traps bacteria. Transcriptomic analyses identify a global state of inflammation in the terrestrialized lungfish skin characterized by granulocyte recruitment. Recruited granulocytes transmigrate into the cocoon where they release extracellular traps. In vivo DNase I surface spraying during terrestrialization results in dysbiosis, septicemia, skin wounds, and hemorrhages. Thus, lungfish have evolved unique immunological adaptations to protect their bodies from infection for extended periods of time while living on land. Trapping bacteria outside their bodies may benefit estivating vertebrates that undergo metabolic torpor.

Prediction of Genes That Function in Methanogenesis and CO2 Pathways in Extremophiles

Gaet’ale (GAL) and Mud’ara (MUP) are two hypersaline ponds located in the Danakil Depression recharged by underground water from the surrounding highlands. These two ponds have different pH, salinity, and show variation in the concentration of many ionic components. Metagenomic analysis concludes that GAL is dominated by bacteria as in the case of the other hypersaline and acidic ponds in the Danakil Depression. However, Archaea dominated the ponds of MUP. In the current study, the application of SEED and KEGG helped to map the ordered steps of specific enzyme catalyzed reaction in converting CO₂ into cell products. We predict that highly efficient and light-independent carbon fixation involving phosphoenolpyruvate carboxylase takes place in MUP. On the contrary, genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis appeared solely in ponds of GAL, implying the biological source of the hazardous methane gas in that environment. Based on the investigation of the sources of the genes of interest, it is clear that cooperative interactions between members of the two communities and syntrophic metabolism is the main strategy adapted to utilize inorganic carbon as a carbon source in both MUP and GAL. This insight can be used to design biotechnological applications of microbial communities in production of methane biogas or to minimize CO₂ emissions.

In silico determination of nitrogen metabolism in microbes from extreme conditions using metagenomics

The acid ponds of the Danakil Depression in northern Ethiopia are polyextreme environments that exceed the normal physicochemical limits of pH, salinity, ion content, and temperature. We tested for the occurrence of DNA-based life in this environment using Metagenomic Shotgun DNA sequencing approaches. The obtained sequences were examined by the bioinformatic tools MetaSpades, DIAMOND and MEGAN 6-CE, and we were able to bin more than 90% of the metagenomics contigs of Dallol and Black Water to the Bacteria domain, and to the Proteobacteria phylum. Predictions of gene function based on SEED disclosed the presence of different nutrient cycles in the acid ponds. For this study, we focused on partial or completely sequenced genes involved in nitrogen metabolism. The KEGG nitrogen metabolism pathway mapping results for both acid ponds showed that all the predicted genes are involved directly or indirectly in the assimilation of ammonia and no dissimilation or nitrification process was identified. Furthermore, the deduced nitrogen fixation in the two acid ponds based on SEED classification indicated the presence of different sets of nitrogen fixing (nif) genes for biosynthesis and maturation of nitrogenase. Based on the in silico analysis, the predicted proteins involved in nitrogen fixation, especially the cysteine desulfurase and [4Fe-4S] ferredoxin, from both acid ponds are unique with less than 80% sequence similarity to the next closest protein sequence. Considering the extremity of the environmental conditions of the two acid ponds in the Danakil depression, this metagenomics dataset can add to the study of unique gene functions in nitrogen metabolism that enable thriving biocommunities in hypersaline and highly acidic conditions.

Effects of ploidy and salmonid alphavirus infection on the skin and gill microbiome of Atlantic salmon (Salmo salar)

The microbial communities that live in symbiosis with the mucosal surfaces of animals provide the host with defense strategies against pathogens. These microbial communities are largely shaped by the environment and the host genetics. Triploid Atlantic salmon (Salmo salar) are being considered for aquaculture as they are reproductively sterile and thus cannot contaminate the natural gene pool. It has not been previously investigated how the microbiome of triploid salmon compares to that of their diploid counterparts. In this study, we compare the steady-state skin and gill microbiome of both diploid and triploid salmon, and determine the effects of salmonid alphavirus 3 experimental infection on their microbial composition. Our results show limited differences in the skin-associated microbiome between triploid and diploid salmon, irrespective of infection. In the gills, we observed a high incidence of the bacterial pathogen Candidatus Branchiomonas, with higher abundance in diploid compared to triploid control fish. Diploid salmon infected with SAV3 showed greater histopathological signs of epitheliocystis compared to controls, a phenomenon not observed in triploid fish. Our results indicate that ploidy can affect the alpha diversity of the gills but not the skin-associated microbial community. Importantly, during a natural outbreak of Branchiomonas sp. the gill microbiome of diploid Atlantic salmon became significantly more dominated by this pathogen than in triploid animals. Thus, our results suggest that ploidy may play a role on Atlantic salmon gill health and provide insights into co-infection with SAV3 and C. Branchiomonas in Atlantic salmon.

Lithogenic hydrogen supports microbial primary production in subglacial and proglacial environments

Life in environments devoid of photosynthesis, such as on early Earth or in contemporary dark subsurface ecosystems, is supported by chemical energy. How, when, and where chemical nutrients released from the geosphere fuel chemosynthetic biospheres is fundamental to understanding the distribution and diversity of life, both today and in the geologic past. Hydrogen (H₂) is a potent reductant that can be generated when water interacts with reactive components of mineral surfaces such as silicate radicals and ferrous iron. Such reactive mineral surfaces are continually generated by physical comminution of bedrock by glaciers. Here, we show that dissolved H₂ concentrations in meltwaters from an iron and silicate mineral-rich basaltic glacial catchment were an order of magnitude higher than those from a carbonate-dominated catchment. Consistent with higher H₂ abundance, sediment microbial communities from the basaltic catchment exhibited significantly shorter lag times and faster rates of net H₂ oxidation and dark carbon dioxide (CO₂) fixation than those from the carbonate catchment, indicating adaptation to use H₂ as a reductant in basaltic catchments. An enrichment culture of basaltic sediments provided with H₂, CO₂, and ferric iron produced a chemolithoautotrophic population related to Rhodoferax ferrireducens with a metabolism previously thought to be restricted to (hyper)thermophiles and acidophiles. These findings point to the importance of physical and chemical weathering processes in generating nutrients that support chemosynthetic primary production. Furthermore, they show that differences in bedrock mineral composition can influence the supplies of nutrients like H₂ and, in turn, the diversity, abundance, and activity of microbial inhabitants.

Specialization of mucosal immunoglobulins in pathogen control and microbiota homeostasis occurred early in vertebrate evolution

Although mammalian secretory immunoglobulin A (sIgA) targets mucosal pathogens for elimination, its interaction with the microbiota also enables commensal colonization and homeostasis. This paradoxical requirement in the control of pathogens versus microbiota raised the question of whether mucosal (secretory) Igs (sIgs) evolved primarily to protect mucosal surfaces from pathogens or to maintain microbiome homeostasis. To address this central question, we used a primitive vertebrate species (rainbow trout) in which we temporarily depleted its mucosal Ig (sIgT). Fish devoid of sIgT became highly susceptible to a mucosal parasite and failed to develop compensatory IgM responses against it. IgT depletion also induced a profound dysbiosis marked by the loss of sIgT-coated beneficial taxa, expansion of pathobionts, tissue damage, and inflammation. Restitution of sIgT levels in IgT-depleted fish led to a reversal of microbial translocation and tissue damage, as well as to restoration of microbiome homeostasis. Our findings indicate that specialization of sIgs in pathogen and microbiota control occurred concurrently early in evolution, thus revealing primordially conserved principles under which primitive and modern sIgs operate in the control of microbes at mucosal surfaces.

Got Glycogen?: Development and Multispecies Validation of the Novel Preserve, Precipitate, Lyse, Precipitate, Purify (PPLPP) Workflow for Environmental DNA Extraction from Longmire's Preserved Water Samples

Unfiltered and filtered water samples can be used to collect environmental DNA (eDNA). We developed the novel "Preserve, Precipitate, Lyse, Precipitate, Purify" (PPLPP) workflow to efficiently extract eDNA from Longmire's preserved unfiltered and filtered water samples (44-100% recovery). The PPLPP workflow includes initial glycogen-aided isopropanol precipitation, guanidium hypochlorite and Triton X-100-based lysis, terminal glycogen-aided polyethylene glycol precipitation, and inhibitor purification. Three novel eDNA assays that exclusively target species invasive to Australia were also developed: Tilapia_v2_16S concurrently targets Oreochromis mossambicus (Mozambique tilapia) and Tilapia mariae (spotted tilapia) while R.marina_16S and C.caroliniana_matK discretely target Rhinella marina (cane toad) and Cabomba caroliniana (fanwort), respectively. All 3 assays were validated in silico before in vitro and in situ validations using PPLPP workflow extracted samples. PPLPP workflow was concurrently validated in vitro and in situ using all 3 assays. In vitro validations demonstrated that 1) glycogen inclusion increased extracellular DNA recovery by ∼48-fold compared with glycogen exclusion, 2) swinging-bucket centrifugation for 90 min at 3270 g is equivalent to fixed-angle centrifugation for 5-20 min at 6750 g, and 3) Zymo OneStep Inhibitor Removal Kit, Qiagen DNeasy PowerClean Pro Cleanup Kit, and silica-Zymo double purification provide effective inhibitor removal. In situ validation demonstrated 95.8 ± 2.8% (mean ± SEM) detectability across all 3 target species in Longmire's preserved unfiltered and filtered water samples extracted using the PPLPP workflow (without phenol:chloroform:isoamyl alcohol purification) after 39 d of incubation at room temperature and 50°C. PPLPP workflow is recommended for future temperate and tropical eDNA studies that use Longmire's to preserve unfiltered or filtered water samples.

Isotopic and genetic methods reveal the role of the gut microbiome in mammalian host essential amino acid metabolism

Intestinal microbiota perform many functions for their host, but among the most important is their role in metabolism, especially the conversion of recalcitrant biomass that the host is unable to digest into bioavailable compounds. Most studies have focused on the assistance gut microbiota provide in the metabolism of carbohydrates, however, their role in host amino acid metabolism is poorly understood. We conducted an experiment on Mus musculus using 16S rRNA gene sequencing and carbon isotope analysis of essential amino acids (AA_ESS) to quantify the community composition of gut microbiota and the contribution of carbohydrate carbon used by the gut microbiome to synthesize AA_ESS that are assimilated by mice to build skeletal muscle tissue. The relative abundances of Firmicutes and Bacteroidetes inversely varied as a function of dietary macromolecular content, with Firmicutes dominating when mice were fed low-protein diets that contained the highest proportions of simple carbohydrates (sucrose). Mixing models estimated that the microbial contribution of AA_ESS to mouse muscle varied from less than 5% (threonine, lysine, and phenylalanine) to approximately 60% (valine) across diet treatments, with the Firmicute-dominated microbiome associated with the greatest contribution. Our results show that intestinal microbes can provide a significant source of the AA_ESS their host uses to synthesize structural tissues. The role that gut microbiota play in the amino acid metabolism of animals that consume protein-deficient diets is likely a significant but under-recognized aspect of foraging ecology and physiology.

A practical guide to sample preservation and pre-PCR processing of aquatic environmental DNA

Environmental DNA (eDNA) is rapidly growing in popularity as a tool for community assessments and species detection. While eDNA approaches are now widely applied, there is not yet agreement on best practices for sample collection and processing. Investigators looking to integrate eDNA approaches into their research programme are required to examine a growing collection of disparate studies to make an often uncertain decision about which protocols best fit their needs. To promote the application of eDNA approaches and to encourage the generation of high-quality data, here we review the most common techniques for the collection, preservation and extraction of metazoan eDNA from water samples. Specifically, we focus on experimental studies that compare various methods and outline the numerous challenges associated with eDNA. While the diverse applications of eDNA do not lend themselves to a one-size-fits-all recommendation, in most cases, capture/concentration of eDNA on cellulose nitrate filters (with pore size determined by water turbidity), followed by storage of filters in Longmire's buffer and extraction with a DNeasy Blood & Tissue Kit (or similar) has been shown to provide sufficient, high-quality DNA. However, we also emphasize the importance of testing and optimizing protocols for the system of interest.

Targeted ITS1 sequencing unravels the mycodiversity of deep-sea sediments from the Gulf of Mexico

Fungi from marine environments have been significantly less studied than terrestrial fungi. This study describes distribution patterns and associated habitat characteristics of the mycobiota of deep-sea sediments collected from the Mexican exclusive economic zone (EEZ) of the Gulf of Mexico (GoM), ranging between 1000 and > 3500 m depth. Internal Transcribed Spacer 1 (ITS1) amplicons were sequenced by Illumina MiSeq. From 29 stations sampled across three annual campaigns, a total of 4421 operational taxonomic units (OTUs) were obtained, indicating a high fungal richness. Most OTUs assignments corresponded to Ascomycota, unidentified fungi and Basidiomycota. The majority of the stations shared a mere 31 OTUs, including the worldwide reported genera Penicillium, Rhodotorula and Cladosporium. Both a transient and a conserved community were identified, suggesting their dependence on or adaptation to the habitat dynamics, respectively. The differences found in fungal richness and taxonomic compositions were correlated principally with latitude, carbon and carbonates content, and terrigenous content, which could be the potential drivers that delimit fungal distribution. This study represents an expansion of our current knowledge on the biogeography of the fungal community from deep-sea sediments, and identifies the geographic and physicochemical properties that delimit fungal composition and distribution in the GoM.

Microbial assemblages reflect environmental heterogeneity in alpine streams

Alpine streams are dynamic habitats harboring substantial biodiversity across small spatial extents. The diversity of alpine stream biota is largely reflective of environmental heterogeneity stemming from varying hydrological sources. Globally, alpine stream diversity is under threat as meltwater sources recede and stream conditions become increasingly homogeneous. Much attention has been devoted to macroinvertebrate diversity in alpine headwaters, yet to fully understand the breadth of climate change threats, a more thorough accounting of microbial diversity is needed. We characterized microbial diversity (specifically Bacteria and Archaea) of 13 streams in two disjunct Rocky Mountain subranges through 16S rRNA gene sequencing. Our study encompassed the spectrum of alpine stream sources (glaciers, snowfields, subterranean ice, and groundwater) and three microhabitats (ice, biofilms, and streamwater). We observed no difference in regional (γ) diversity between subranges but substantial differences in diversity among (β) stream types and microhabitats. Within-stream (α) diversity was highest in groundwater-fed springs, lowest in glacier-fed streams, and positively correlated with water temperature for both streamwater and biofilm assemblages. We identified an underappreciated alpine stream type-the icy seep-that are fed by subterranean ice, exhibit cold temperatures (summer mean <2°C), moderate bed stability, and relatively high conductivity. Icy seeps will likely be important for combatting biodiversity losses as they contain similar microbial assemblages to streams fed by surface ice yet may be buffered against climate change by insulating debris cover. Our results show that the patterns of microbial diversity support an ominous trend for alpine stream biodiversity; as meltwater sources decline, stream communities will become more diverse locally, but regional diversity will be lost. Icy seeps, however, represent a source of optimism for the future of biodiversity in these imperiled ecosystems.

Robust sampling and preservation of DNA for microbial community profiling in field experiments

Objective

Stabilising samples of microbial communities for DNA extraction without access to laboratory equipment can be a challenging task. In this paper we propose a method using filter paper disks for the preservation of DNA from diverse microbial communities which are found in a fermented milk product.

Results

Small adaptations to the DNA extraction method used for liquid fermented milk delivered DNA of sufficient amounts and quality to be used for later analyses, e.g. full community 16S amplicon sequencing. The microbial community structure obtained via the filter paper method showed sufficient resemblance to the structure obtain via the traditional DNA extraction from the liquid milk sample. This method can therefore successfully be used to analyse diverse microbial communities from fermented milk products from remote areas.

Electronic supplementary material

The online version of this article (10.1186/s13104-019-4187-2) contains supplementary material, which is available to authorized users.

Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss)

Commensal microorganisms present at mucosal surfaces play a vital role in protecting the host organism from bacterial infection. There are multiple factors that contribute to selecting for the microbiome, including host genetics. Flavobacterium psychrophilum, the causative agent of Bacterial Cold Water Disease in salmonids, accounts for acute losses in wild and farmed rainbow trout (Oncorhynchus mykiss). The U.S. National Center for Cool and Cold Water Aquaculture has used family-based selective breeding to generate a line of rainbow trout with enhanced resistance to F. psychrophilum. The goal of this study is to determine whether selective breeding impacts the gut and gill microbiome of the F. psychrophilum-resistant as compared to a background matched susceptible trout line. Mid-gut and gill samples were collected from juvenile fish maintained at high or low stocking densities and microbial diversity assessed by 16S rDNA amplicon sequencing. Results indicate that alpha diversity was significantly higher in the mid-gut of the susceptible line compared to the resistant line, while no significant differences in alpha diversity were observed in the gills. Mycoplasma sp. was the dominant taxon in the mid-gut of both groups, although it was present at a decreased abundance in the susceptible line. We also observed an increased abundance of the potential opportunistic pathogen Brevinema andersonii in the susceptible line. Within the gills, both lines exhibited similar microbial profiles, with Candidatus Branchiomonas being the dominant taxon. Together, these results suggest that selectively bred F. psychrophilum-resistant trout may harness a more resilient gut microbiome, attributing to the disease resistant phenotype. Importantly, interactions between host genetics and environmental factors such as stocking density have a significant impact in shaping trout microbial communities.

Local and Regional Scale Heterogeneity Drive Bacterial Community Diversity and Composition in a Polar Desert

The distribution of organisms in an environment is neither uniform nor random but is instead spatially patterned. The factors that control this patterning are complex and the underlying mechanisms are poorly understood. Soil microbes are critical to ecosystem function but exhibit highly complex distributions and community dynamics due in large part to the scale-dependent effects of environmental heterogeneity. To better understand the impact of environmental heterogeneity on the distribution of soil microbes, we sequenced the 16S rRNA gene from bacterial communities in the microbe-dominated polar desert ecosystem of the McMurdo Dry Valleys (MDV), Antarctica. Significant differences in key edaphic variables and alpha diversity were observed among the three lake basins of the Taylor Valley (Kruskal-Wallis; pH: χ2 = 68.89, P < 0.001, conductivity: χ2 = 35.03, P < 0.001, observed species: χ2 = 7.98, P = 0.019 and inverse Simpson: χ2 = 18.52, P < 0.001) and each basin supported distinctive microbial communities (ANOSIM R = 0.466, P = 0.001, random forest ratio of 14.1). However, relationships between community structure and edaphic characteristics were highly variable and contextual, ranging in magnitude and direction across regional, basin, and local scales. Correlations among edaphic factors (pH and soil conductivity) and the relative abundance of specific phyla were most pronounced along local environmental gradients in the Lake Fryxell basin where Acidobacteria, Bacteroidetes, and Proteobacteria declined while Deinococcus-Thermus and Gemmatimonadetes increased with soil conductivity (all P < 0.1). Species richness was most strongly related to the soil conductivity gradient present within this study system. We suggest that the relative importance of pH versus soil conductivity in structuring microbial communities is related to the length of edaphic gradients and the spatial scale of sampling. These results highlight the importance of conducting studies over large ranges of key environmental gradients and across multiple spatial scales to assess the influence of environmental heterogeneity on the composition and diversity of microbial communities.

A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing

Obtaining high-quality plant materials for experiments is challenging for many research projects. Therefore, it is of special importance to determine the best method for preserving biological macromolecules like DNA, which degrade over time. Although some research has demonstrated that DNA degradation has little effect on traditional molecular markers, the effects of DNA degradation on ddRAD-seq, a popular reduced-representation sequencing technology, have not been adequately investigated. In this study, we first chose six woody bamboo species (Bambusoideae, Poaceae) to explore appropriate methods for preserving molecular materials with two DNA extraction approaches. Then we sequenced twenty-one bamboos and examined the effects of DNA quality on data generation using the ddRAD-seq technique (MiddRAD-seq). Finally, we reconstructed phylogenies of twenty woody bamboo species. We found that the integrity of dry-powdered DNA was preserved longer than that of TE-dissolved DNA, regardless of whether the DNA was extracted by a modified CTAB protocol or DNAsecure plant kit. The ddRAD-seq data were robust, except when DNA was severely degraded. In addition, we resolved the phylogenetic positions of the sampled Phyllostachys spp. Our results suggest that dry-powdered DNA is the most appropriate preservation method for plant molecular materials. Furthermore, a moderate level of DNA degradation has little effect on reduced representation sequencing techniques represented by ddRAD-seq.

Salt Marsh Bacterial Communities before and after the Deepwater Horizon Oil Spill

Coastal salt marshes along the northern Gulf of Mexico shoreline received varied types and amounts of weathered oil residues after the 2010 Deepwater Horizon oil spill. At the time, predicting how marsh bacterial communities would respond and/or recover to oiling and other environmental stressors was difficult because baseline information on community composition and dynamics was generally unavailable. Here, we evaluated marsh vegetation, physicochemistry, flooding frequency, hydrocarbon chemistry, and subtidal sediment bacterial communities from 16S rRNA gene surveys at 11 sites in southern Louisiana before the oil spill and resampled the same marshes three to four times over 38 months after the spill. Calculated hydrocarbon biomarker indices indicated that oil replaced native natural organic matter (NOM) originating from Spartina alterniflora and marine phytoplankton in the marshes between May 2010 and September 2010. At all the studied marshes, the major class- and order-level shifts among the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria occurred within these first 4 months, but another community shift occurred at the time of peak oiling in 2011. Two years later, hydrocarbon levels decreased and bacterial communities became more diverse, being dominated by Alphaproteobacteria (Rhizobiales), Chloroflexi (Dehalococcoidia), and Planctomycetes Compositional changes through time could be explained by NOM source differences, perhaps due to vegetation changes, as well as marsh flooding and salinity excursions linked to freshwater diversions. These findings indicate that persistent hydrocarbon exposure alone did not explain long-term community shifts.IMPORTANCE Significant deterioration of coastal salt marshes in Louisiana has been linked to natural and anthropogenic stressors that can adversely affect how ecosystems function. Although microorganisms carry out and regulate most biogeochemical reactions, the diversity of bacterial communities in coastal marshes is poorly known, with limited investigation of potential changes in bacterial communities in response to various environmental stressors. The Deepwater Horizon oil spill provided an unprecedented opportunity to study the long-term effects of an oil spill on microbial systems in marshes. Compared to previous studies, the significance of our research stems from (i) a broader geographic range of studied marshes, (ii) an extended time frame of data collection that includes prespill conditions, (iii) a more accurate procedure using biomarker indices to understand oiling, and (iv) an examination of other potential stressors linked to in situ environmental changes, aside from oil exposure.

Decoupled responses of soil bacteria and their invertebrate consumer to warming, but not freeze-thaw cycles, in the Antarctic Dry Valleys

Altered temperature profiles resulting in increased warming and freeze-thaw cycle (FTC) frequency pose great ecological challenges to organisms in alpine and polar ecosystems. We performed a laboratory microcosm experiment to investigate how temperature variability affects soil bacterial cell numbers, and abundance and traits of soil microfauna (the microbivorous nematode Scottnema lindsayae) from McMurdo Dry Valleys, Antarctica. FTCs and constant freezing shifted nematode body size distribution towards large individuals, driven by higher mortality among smaller individuals. FTCs reduced both bacterial and nematode abundance, but bacterial cell numbers also declined under warming, demonstrating decoupled consumer-prey responses. We predict that higher occurrence of FTCs in cold ecosystems will select for large body size within soil microinvertebrates and overall reduce their abundance. In contrast, warm temperatures without FTCs could lead to divergent responses in soil bacteria and their microinvertebrate consumers, potentially affecting energy and nutrient transfer rates in soil food webs of cold ecosystems.

Primary productivity as a control over soil microbial diversity along environmental gradients in a polar desert ecosystem

Primary production is the fundamental source of energy to foodwebs and ecosystems, and is thus an important constraint on soil communities. This coupling is particularly evident in polar terrestrial ecosystems where biological diversity and activity is tightly constrained by edaphic gradients of productivity (e.g., soil moisture, organic carbon availability) and geochemical severity (e.g., pH, electrical conductivity). In the McMurdo Dry Valleys of Antarctica, environmental gradients determine numerous properties of soil communities and yet relatively few estimates of gross or net primary productivity (GPP, NPP) exist for this region. Here we describe a survey utilizing pulse amplitude modulation (PAM) fluorometry to estimate rates of GPP across a broad environmental gradient along with belowground microbial diversity and decomposition. PAM estimates of GPP ranged from an average of 0.27 μmol O2/m2/s in the most arid soils to an average of 6.97 μmol O2/m2/s in the most productive soils, the latter equivalent to 217 g C/m2/y in annual NPP assuming a 60 day growing season. A diversity index of four carbon-acquiring enzyme activities also increased with soil productivity, suggesting that the diversity of organic substrates in mesic environments may be an additional driver of microbial diversity. Overall, soil productivity was a stronger predictor of microbial diversity and enzymatic activity than any estimate of geochemical severity. These results highlight the fundamental role of environmental gradients to control community diversity and the dynamics of ecosystem-scale carbon pools in arid systems.

Leaf endophytic fungus interacts with precipitation to alter belowground microbial communities in primary successional dunes

Understanding interactions between above- and belowground components of ecosystems is an important next step in community ecology. These interactions may be fundamental to predicting ecological responses to global change because indirect effects occurring through altered species interactions can outweigh or interact with the direct effects of environmental drivers. In a multiyear field experiment (2010-2015), we tested how experimental addition of a mutualistic leaf endophyte (Epichloë amarillans) associated with American beachgrass (Ammophila breviligulata) interacted with an altered precipitation regime (±30%) to affect the belowground microbial community. Epichloë addition increased host root biomass at the plot scale, but reduced the length of extraradical arbuscular mycorrhizal (AM) fungal hyphae in the soil. Under ambient precipitation alone, the addition of Epichloë increased root biomass per aboveground tiller and reduced the diversity of AM fungi in A. breviligulata roots. Furthermore, with Epichloë added, the diversity of root-associated bacteria declined with higher soil moisture, whereas in its absence, bacterial diversity increased with higher soil moisture. Thus, the aboveground fungal mutualist not only altered the abundance and composition of belowground microbial communities but also affected how belowground communities responded to climate, suggesting that aboveground microbes have potential for cascading influences on community dynamics and ecosystem processes that occur belowground.

Salmonid alphavirus infection causes skin dysbiosis in Atlantic salmon (Salmo salar L.) post-smolts

Interactions among host, microbiota and viral pathogens are complex and poorly understood. The goal of the present study is to assess the changes in the skin microbial community of Atlantic salmon (Salmo salar L.) in response to experimental infection with salmonid alphavirus (SAV). The salmon skin microbial community was determined using 16S rDNA pyrosequencing in five different experimental groups: control, 7 days after infection with low-dose SAV, 14 days after infection with low-dose SAV, 7 days after infection with high-dose SAV, and 14 days after infection with high-dose SAV. Both infection treatment and time after infection were strong predictors of the skin microbial community composition. Skin samples from SAV3 infected fish showed an unbalanced microbiota characterized by a decreased abundance of Proteobacteria such as Oleispira sp. and increased abundances of opportunistic taxa including Flavobacteriaceae, Streptococcaceae and Tenacibaculum sp. These results demonstrate that viral infections can result in skin dysbiosis likely rendering the host more susceptible to secondary bacterial infections.

Microbial community analysis of pH 4 thermal springs in Yellowstone National Park

The pH of the majority of thermal springs in Yellowstone National Park (YNP) is from 1 to 3 and 6 to 10; relatively few springs (~5%) have a pH range of 4-5. We used 16S rRNA gene pyrosequencing to investigate microbial communities sampled from four pH 4 thermal springs collected from four regions of YNP that differed in their fluid temperature and geochemistry. Our results revealed that the composition of bacterial communities varied among the sites, despite sharing similar pH values. The taxonomic composition and metabolic functional potential of the site with the lowest temperature (55 °C), a thermal spring from the Seven Mile Hole (SMH) area, were further investigated using shotgun metagenome sequencing. The taxonomic classification, based on 372 Mbp of unassembled metagenomic reads, indicated that this community included a high proportion of Chloroflexi, Bacteroidetes, Proteobacteria, and Firmicutes. Functional comparison with other YNP thermal spring metagenomes indicated that the SMH metagenome was enriched in genes related to energy production and conversion, transcription, and carbohydrate transport. Analysis of genes involved in nitrogen metabolism revealed assimilatory and dissimilatory nitrate reduction pathways, whereas the majority of genes involved in sulfur metabolism were related to the reduction of sulfate to adenylylsulfate, sulfite, and H₂S. Given that pH 4 thermal springs are relatively less common in YNP and thermal areas worldwide, they may harbor novel microbiota and the communities that inhabit them deserve further investigation.

Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes

Microbial populations living in environments with temperatures above 50°C (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. Since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. The integrated study of the whole-community DNA from an environment, known as metagenomics, coupled with the development of next generation sequencing (NGS) technologies, has allowed the generation of large amounts of data from thermophiles. In this review, we summarize the main approaches commonly utilized for assessing the taxonomic and functional diversity of thermophiles through metagenomics, including several bioinformatics tools and some metagenome-derived methods to isolate their thermozymes.

Patterns of bacterial biodiversity in the glacial meltwater streams of the McMurdo Dry Valleys, Antarctica

Microbial consortia dominate glacial meltwater streams from polar regions, including the McMurdo Dry Valleys (MDV), where they thrive under physiologically stressful conditions. In this study, we examined microbial mat types and sediments found in 12 hydrologically diverse streams to describe the community diversity and composition within and across sites. Sequencing of the 16S rRNA gene from 129 samples revealed ∼24 000 operational taxonomic units (<97% DNA similarity), making streams the most biodiverse habitat in the MDV. Principal coordinate analyses revealed significant but weak clustering by mat type across all streams (ANOSIM R-statistic = 0.28) but stronger clustering within streams (ANOSIM R-statistic from 0.28 to 0.94). Significant relationships (P < 0.05) were found between bacterial diversity and mat ash-free dry mass, suggesting that diversity is related to the hydrologic regimes of the various streams, which are predictive of mat biomass. However, correlations between stream chemistry and community members were weak, possibly reflecting the importance of internal processes and hydrologic conditions. Collectively, these results suggest that localized conditions dictate bacterial community composition of the same mat types and sediments from different streams, and while MDV streams are hotspots of biodiversity in an otherwise depauperate landscape, controls on community structure are complex and site specific.

Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica

The soils of the McMurdo Dry Valleys, Antarctica are an extreme polar desert, inhabited exclusively by microscopic taxa. This region is on the threshold of anticipated climate change, with glacial melt, permafrost thaw, and the melting of massive buried ice increasing liquid water availability and mobilizing soil nutrients. Experimental water and organic matter (OM) amendments were applied to investigate how these climate change effects may impact the soil communities. To identify active taxa and their functions, total community RNA transcripts were sequenced and annotated, and amended soils were compared with unamended control soils using differential abundance and expression analyses. Overall, taxonomic diversity declined with amendments of water and OM. The domain Bacteria increased with both amendments while Eukaryota declined from 38% of all taxa in control soils to 8 and 11% in water and OM amended soils, respectively. Among bacterial phyla, Actinobacteria (59%) dominated water-amended soils and Firmicutes (45%) dominated OM amended soils. Three bacterial phyla (Actinobacteria, Proteobacteria, and Firmicutes) were primarily responsible for the observed positive functional responses, while eukaryotic taxa experienced the majority (27 of 34) of significant transcript losses. These results indicated that as climate changes in this region, a replacement of endemic taxa adapted to dry, oligotrophic conditions by generalist, copiotrophic taxa is likely.

Nutrient treatments alter microbial mat colonization in two glacial meltwater streams from the McMurdo Dry Valleys, Antarctica

Microbial mats are abundant in many alpine and polar aquatic ecosystems. With warmer temperatures, new hydrologic pathways are developing in these regions and increasing dissolved nutrient fluxes. In the McMurdo Dry Valleys, thermokarsting may release both nutrients and sediment, and has the potential to influence mats in glacial meltwater streams. To test the role of nutrient inputs on community structure, we created nutrient diffusing substrata (NDS) with agar enriched in N, P and N + P, with controls, and deployed them into two Dry Valley streams. We found N amendments (N and N + P) to have greater chlorophyll-a concentrations, total algal biovolume, more fine filamentous cyanobacteria and a higher proportion of live diatoms than other treatments. Furthermore, N treatments were substantially elevated in Bacteroidetes and the small diatom, Fistulifera pelliculosa. On the other hand, species richness was almost double in P and N + P treatments over others, and coccoid green algae and Proteobacteria were more abundant in both streams. Collectively, these data suggest that nutrients have the potential to stimulate growth and alter community structure in glacial meltwater stream microbial mats, and the recent erosion of permafrost and accelerated glacial melt will likely impact resident biota in polar lotic systems here and elsewhere.

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes(1). Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface(2-4), the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63-90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H2 oxidation (or H2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere.

Use of Serial Quantitative PCR of the vapA Gene of Rhodococcus equi in Feces for Early Detection of R. equi Pneumonia in Foals

BACKGROUND

Current screening tests for Rhodococcus equi pneumonia in foals lack adequate accuracy for clinical use. Real-time, quantitative PCR (qPCR) for virulent R. equi in feces has not been systematically evaluated as a screening test.

OBJECTIVE

The objective of this study was to evaluate the accuracy of qPCR for vapA in serially collected fecal samples as a screening test for R. equi pneumonia in foals.

ANIMALS

One hundred and twenty-five foals born in 2011 at a ranch in Texas.

METHODS

Fecal samples were collected concurrently with thoracic ultrasonography (TUS) screening examinations at ages 3, 5, and 7 weeks. Affected (pneumonic) foals (n = 25) were matched by age and date-of-birth to unaffected (n = 25) and subclinical (ie, having thoracic TUS lesions but no clinical signs of pneumonia) foals (n = 75). DNA was extracted from feces using commercial kits and concentration of virulent R. equi in feces was determined by qPCR.

RESULTS

Subsequently affected foals had significantly greater concentrations of vapA in feces than foals that did not develop pneumonia (unaffected and subclinical foals) at 5 and 7 weeks of age. Accuracy of fecal qPCR, however, was poor as a screening test to differentiate foals that would develop clinical signs of pneumonia from those that would remain free of clinical signs (including foals with subclinical pulmonary lesions attributed to R. equi) using receiver operating characteristic (ROC) methods.

CONCLUSIONS AND CLINICAL IMPORTANCE

In the population studied, serial qPCR on feces lacked adequate accuracy as a screening test for clinical R. equi foal pneumonia.

Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin

The mucosal surfaces of wild and farmed aquatic vertebrates face the threat of many aquatic pathogens, including fungi. These surfaces are colonized by diverse symbiotic bacterial communities that may contribute to fight infection. Whereas the gut microbiome of teleosts has been extensively studied using pyrosequencing, this tool has rarely been employed to study the compositions of the bacterial communities present on other teleost mucosal surfaces. Here we provide a topographical map of the mucosal microbiome of an aquatic vertebrate, the rainbow trout (Oncorhynchus mykiss). Using 16S rRNA pyrosequencing, we revealed novel bacterial diversity at each of the five body sites sampled and showed that body site is a strong predictor of community composition. The skin exhibited the highest diversity, followed by the olfactory organ, gills, and gut. Flectobacillus was highly represented within skin and gill communities. Principal coordinate analysis and plots revealed clustering of external sites apart from internal sites. A highly diverse community was present within the epithelium, as demonstrated by confocal microscopy and pyrosequencing. Using in vitro assays, we demonstrated that two Arthrobacter sp. skin isolates, a Psychrobacter sp. strain, and a combined skin aerobic bacterial sample inhibit the growth of Saprolegnia australis and Mucor hiemalis, two important aquatic fungal pathogens. These results underscore the importance of symbiotic bacterial communities of fish and their potential role for the control of aquatic fungal diseases.

Influence of anode surface chemistry on microbial fuel cell operation

Self-assembled monolayers (SAMs) modified gold anodes are used in single chamber microbial fuel cells for organic removal and electricity generation. Hydrophilic (N(CH3)3(+), OH, COOH) and hydrophobic (CH3) SAMs are examined for their effect on bacterial attachment, current and power output. The different substratum chemistry affects the community composition of the electrochemically active biofilm formed and thus the current and power output. Of the four SAM-modified anodes tested, N(CH3)3(+) results in the shortest start up time (15 days), highest current achieved (225 μA cm(-2)) and highest MFC power density (40 μW cm(-2)), followed by COOH (150 μA cm(-2) and 37 μW cm(-2)) and OH (83 μA cm(-2) and 27 μW cm(-2)) SAMs. Hydrophobic SAM decreases electrochemically active bacteria attachment and anode performance in comparison to hydrophilic SAMs (CH3 modified anodes 7 μA cm(-2) anodic current and 1.2 μW cm(-2) MFC's power density). A consortium of Clostridia and δ-Proteobacteria is found on all the anode surfaces, suggesting a synergistic cooperation under anodic conditions.

Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian bigheaded carp (Hypophthalmichthys spp.)

Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.

Improved group-specific primers based on the full SILVA 16S rRNA gene reference database

Quantitative PCR (qPCR) and community fingerprinting methods, such as the Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis,are well-suited techniques for the examination of microbial community structures. The use of phylum and class-specific primers can provide enhanced sensitivity and phylogenetic resolution as compared with domain-specific primers. To date, several phylum- and class-specific primers targeting the 16S ribosomal RNA gene have been published. However, many of these primers exhibit low discriminatory power against non-target bacteria in PCR. In this study, we evaluated the precision of certain published primers in silico and via specific PCR. We designed new qPCR and T-RFLP primer pairs (for the classes Alphaproteobacteria and Betaproteobacteria, and the phyla Bacteroidetes, Firmicutes and Actinobacteria) by combining the sequence information from a public dataset (SILVA SSU Ref 102 NR) with manual primer design. We evaluated the primer pairs via PCR using isolates of the above-mentioned groups and via screening of clone libraries from environmental soil samples and human faecal samples. As observed through theoretical and practical evaluation, the primers developed in this study showed a higher level of precision than previously published primers, thus allowing a deeper insight into microbial community dynamics.

Regime shift in sandy beach microbial communities following Deepwater Horizon oil spill remediation efforts

Sandy beaches support a wide variety of underappreciated biodiversity that is critical to coastal ecosystems. Prior to the 2010 Deepwater Horizon oil spill, the diversity and function of supratidal beach sediment microbial communities along Gulf of Mexico coastlines were not well understood. As such, it was unclear if microbial community compositional changes would occur following exposure to beached oil, if indigenous communities could biodegrade oil, or how cleanup efforts, such as sand washing and sediment redistribution, would impact microbial ecosystem resiliency. Transects perpendicular to the shoreline were sampled from public beaches on Grand Isle, Louisiana, and Dauphin Island, Alabama, over one year. Prior to oil coming onshore, elevated levels of bacteria associated with fecal contamination were detected (e.g., Enterobacteriales and Campylobacterales). Over time, significant shifts within major phyla were identified (e.g., Proteobacteria, Firmicutes, Actinobacteria) and fecal indicator groups were replaced by taxa affiliated with open-ocean and marine systems (e.g., Oceanospirillales, Rhodospirillales, and Rhodobacterales). These new bacterial groups included putative hydrocarbon degraders, similar to those identified near the oil plume offshore. Shifts in the microbial community composition strongly correlated to more poorly sorted sediment and grain size distributional changes. Natural oceanographic processes could not account for the disrupted sediment, especially from the backshore well above the maximum high-tide levels recorded at these sites. Sand washing and tilling occurred on both open beaches from August through at least December 2010, which were mechanisms that could replace fecal indicator groups with open-ocean groups. Consequently, remediation efforts meant to return beaches to pre-spill compositions caused a regime shift that may have added potential ecosystem function, like hydrocarbon degradation, to the sediment. Future research will need to assess the persistence and impact of the newly formed microbial communities to the overall sandy beach ecosystems.

Characterization of growing bacterial populations in McMurdo Dry Valley soils through stable isotope probing with (18) O-water

Soil microbial communities of the McMurdo Dry Valleys, Antarctica (MDV) contain representatives from at least fourteen bacterial phyla. However, given low rates of microbial activity, it is unclear whether this richness represents functioning rather than dormant members of the community. We used stable isotope probing (SIP) with (18) O-water to determine if microbial populations grow in MDV soils. Changes in the microbial community were characterized in soils amended with H2 (18) O and H2 (18) O-organic matter. Sequencing the 16S rRNA genes of the heavy and light fractions of the bacterial community DNA shows that DNA of microbial populations was labeled with (18) O-water, indicating these micro-organisms grew in the MDV soils. Significant differences existed in the community composition of the heavy and light fractions of the H2 (18) O and H2 (18) O-organic matter amended samples (Anosim P < 0.05 of weighted Unifrac distance). Control samples and the light DNA fraction of the H2 (18) O amended samples were dominated by representatives of the phyla Deinococcus-Thermus, Proteobacteria, Planctomyces, Gemmatimonadetes, Actinobacteria and Acidobacteria, whereas Proteobacteria were more prevalent in the heavy DNA fractions from the H2 (18) O-water and the H2 (18) O-water-organic matter treatments. Our results indicate that SIP with H2 (18) O can be used to distinguish active bacterial populations even in this low organic matter environment.

Soil microbial responses to increased moisture and organic resources along a salinity gradient in a polar desert

Microbial communities in extreme environments often have low diversity and specialized physiologies suggesting a limited resistance to change. The McMurdo Dry Valleys (MDV) are a microbially dominated, extreme ecosystem currently undergoing climate change-induced disturbances, including the melting of massive buried ice, cutting through of permafrost by streams, and warming events. These processes are increasing moisture across the landscape, altering conditions for soil communities by mobilizing nutrients and salts and stimulating autotrophic carbon inputs to soils. The goal of this study was to determine the effects of resource addition (water/organic matter) on the composition and function of microbial communities in the MDV along a natural salinity gradient representing an additional gradient of stress in an already extreme environment. Soil respiration and the activity of carbon-acquiring extracellular enzymes increased significantly (P < 0.05) with the addition of resources at the low- and moderate-salinity sites but not the high-salinity site. The bacterial community composition was altered, with an increase in Proteobacteria and Firmicutes with water and organic matter additions at the low- and moderate-salinity sites and a near dominance of Firmicutes at the high-salinity site. Principal coordinate analyses of all samples using a phylogenetically informed distance matrix (UniFrac) demonstrated discrete clustering among sites (analysis of similarity [ANOSIM], P < 0.05 and R > 0.40) and among most treatments within sites. The results from this experimental work suggest that microbial communities in this environment will undergo rapid change in response to the altered resources resulting from climate change impacts occurring in this region.

An analysis of geothermal and carbonic springs in the western United States sustained by deep fluid inputs

Hydrothermal springs harbor unique microbial communities that have provided insight into the early evolution of life, expanded known microbial diversity, and documented a deep Earth biosphere. Mesothermal (cool but above ambient temperature) continental springs, however, have largely been ignored although they may also harbor unique populations of micro-organisms influenced by deep subsurface fluid mixing with near surface fluids. We investigated the microbial communities of 28 mesothermal springs in diverse geologic provinces of the western United States that demonstrate differential mixing of deeply and shallowly circulated water. Culture-independent analysis of the communities yielded 1966 bacterial and 283 archaeal 16S rRNA gene sequences. The springs harbored diverse taxa and shared few operational taxonomic units (OTUs) across sites. The Proteobacteria phylum accounted for most of the dataset (81.2% of all 16S rRNA genes), with 31 other phyla/candidate divisions comprising the remainder. A small percentage (~6%) of bacterial 16S rRNA genes could not be classified at the phylum level, but were mostly distributed in those springs with greatest inputs of deeply sourced fluids. Archaeal diversity was limited to only four springs and was primarily composed of well-characterized Thaumarchaeota. Geochemistry across the dataset was varied, but statistical analyses suggested that greater input of deeply sourced fluids was correlated with community structure. Those with lesser input contained genera typical of surficial waters, while some of the springs with greater input may contain putatively chemolithotrophic communities. The results reported here expand our understanding of microbial diversity of continental geothermal systems and suggest that these communities are influenced by the geochemical and hydrologic characteristics arising from deeply sourced (mantle-derived) fluid mixing. The springs and communities we report here provide evidence for opportunities to understand new dimensions of continental geobiological processes where warm, highly reduced fluids are mixing with more oxidized surficial waters.

Factors Controlling Soil Microbial Biomass and Bacterial Diversity and Community Composition in a Cold Desert Ecosystem: Role of Geographic Scale

Understanding controls over the distribution of soil bacteria is a fundamental step toward describing soil ecosystems, understanding their functional capabilities, and predicting their responses to environmental change. This study investigated the controls on the biomass, species richness, and community structure and composition of soil bacterial communities in the McMurdo Dry Valleys, Antarctica, at local and regional scales. The goals of the study were to describe the relationships between abiotic characteristics and soil bacteria in this unique, microbially dominated environment, and to test the scale dependence of these relationships in a low complexity ecosystem. Samples were collected from dry mineral soils associated with snow patches, which are a significant source of water in this desert environment, at six sites located in the major basins of the Taylor and Wright Valleys. Samples were analyzed for a suite of characteristics including soil moisture, pH, electrical conductivity, soil organic matter, major nutrients and ions, microbial biomass, 16 S rRNA gene richness, and bacterial community structure and composition. Snow patches created local biogeochemical gradients while inter-basin comparisons encompassed landscape scale gradients enabling comparisons of microbial controls at two distinct spatial scales. At the organic carbon rich, mesic, low elevation sites Acidobacteria and Actinobacteria were prevalent, while Firmicutes and Proteobacteria were dominant at the high elevation, low moisture and biomass sites. Microbial parameters were significantly related with soil water content and edaphic characteristics including soil pH, organic matter, and sulfate. However, the magnitude and even the direction of these relationships varied across basins and the application of mixed effects models revealed evidence of significant contextual effects at local and regional scales. The results highlight the importance of the geographic scale of sampling when determining the controls on soil microbial community characteristics.

Do diet and taxonomy influence insect gut bacterial communities?

Many insects contain diverse gut microbial communities. While several studies have focused on a single or small group of species, comparative studies of phylogenetically diverse hosts can illuminate general patterns of host-microbiota associations. In this study, we tested the hypotheses that (i) host diet and (ii) host taxonomy structure intestinal bacterial community composition among insects. We used published 16S rRNA gene sequence data for 58 insect species in addition to four beetle species sampled from the Sevilleta National Wildlife Refuge to test these hypotheses. Overall, gut bacterial species richness in these insects was low. Decaying wood xylophagous insects harboured the richest bacterial gut flora (102.8 species level operational taxonomic units (OTUs)/sample ± 71.7, 11.8 ± 5.9 phylogenetic diversity (PD)/sample), while bees and wasps harboured the least rich bacterial communities (11.0 species level OTUs/sample ± 5.4, 2.6 ± 0.8 PD/sample). We found evidence to support our hypotheses that host diet and taxonomy structure insect gut bacterial communities (P < 0.001 for both). However, while host taxonomy was important in hymenopteran and termite gut community structure, diet was an important community structuring factor particularly for insect hosts that ingest lignocellulose-derived substances. Our analysis provides a baseline comparison of insect gut bacterial communities from which to test further hypotheses concerning proximate and ultimate causes of these associations.

Archaeal and bacterial diversity in hot springs on the Tibetan Plateau, China

The diversity of archaea and bacteria was investigated in ten hot springs (elevation >4600 m above sea level) in Central and Central-Eastern Tibet using 16S rRNA gene phylogenetic analysis. The temperature and pH of these hot springs were 26-81°C and close to neutral, respectively. A total of 959 (415 and 544 for bacteria and archaea, respectively) clone sequences were obtained. Phylogenetic analysis showed that bacteria were more diverse than archaea and that these clone sequences were classified into 82 bacterial and 41 archaeal operational taxonomic units (OTUs), respectively. The retrieved bacterial clones were mainly affiliated with four known groups (i.e., Firmicutes, Proteobacteria, Cyanobacteria, Chloroflexi), which were similar to those in other neutral-pH hot springs at low elevations. In contrast, most of the archaeal clones from the Tibetan hot springs were affiliated with Thaumarchaeota, a newly proposed archaeal phylum. The dominance of Thaumarchaeota in the archaeal community of the Tibetan hot springs appears to be unique, although the exact reasons are not yet known. Statistical analysis showed that diversity indices of both archaea and bacteria were not statistically correlated with temperature, which is consistent with previous studies.