Microbial and Biogeochemical Indicators of Methane in Groundwater Aquifers of the Denver Basin, Colorado.

The presence of methane and other hydrocarbons in domestic-use groundwater aquifers poses significant environmental and human health concerns. Isotopic measurements are often relied upon as indicators of groundwater aquifer contamination with methane. While these parameters are used to infer microbial metabolisms, there is growing evidence that isotopes present an incomplete picture of subsurface microbial processes. This study examined the relationships between microbiology and chemistry in groundwater wells located in the Denver-Julesburg Basin of Colorado, a rapidly urbanizing area with active oil and gas development. A primary goal was to determine if microbial data can reliably indicate the quantities and sources of groundwater methane. Comprehensive chemical and molecular analyses were performed on 39 groundwater well samples from five aquifers. Elevated methane concentrations were found in only one aquifer, and both isotopic and microbial data support a microbial origin. Microbial parameters had similar explanatory power as chemical parameters for predicting sample methane concentrations. Furthermore, a subset of samples with unique microbiology corresponded with unique chemical signatures that may be useful indicators of methane gas migration, potentially from nearby coal seams interacting with the aquifer. Microbial data may allow for more accurate determination of groundwater contamination and improved long-term water quality monitoring compared solely to isotopic and chemical data in areas with microbial methane.

Drifting along: using diatoms to track the contribution of microbial mats to particulate organic matter transport in a glacial meltwater stream in the McMurdo Dry Valleys, Antarctica.

Flow pulses mobilize particulate organic matter (POM) in streams from the surrounding landscape and streambed. This POM serves as a source of energy and nutrients, as well as a means for organismal dispersal, to downstream communities. In the barren terrestrial landscape of the McMurdo Dry Valleys (MDV) of Antarctica, benthic microbial mats occupying different in-stream habitat types are the dominant POM source in the many glacier-fed streams. Many of these streams experience daily flow peaks that mobilize POM, and diatoms recovered from underlying stream sediments suggest that mat-derived diatoms in the POM are retained there through hyporheic exchange. Yet, 'how much' and 'when' different in-stream habitat types contribute to POM diatom assemblages is unknown. To quantify the contribution of different in-stream habitat types to POM diatom assemblages, we collected time-integrated POM samples over four diel experiments, which spanned a gradient of flow conditions over three summers. Diatoms from POM samples were identified, quantified, and compared with dominant habitat types (i.e., benthic 'orange' mats, marginal 'black' mats, and bare sediments). Like bulk POM, diatom cell concentrations followed a clockwise hysteresis pattern with stream discharge over the daily flow cycles, indicating supply limitation. Diatom community analyses showed that different habitat types harbor distinct diatom communities, and mixing models revealed that a substantial proportion of POM diatoms originated from bare sediments during baseflow conditions. Meanwhile, orange and black mats contribute diatoms to POM primarily during daily flow peaks when both cell concentrations and discharge are highest, making mats the most important contributors to POM diatom assemblages at high flows. These observations may help explain the presence of mat-derived diatoms in hyporheic sediments. Our results thus indicate a varying importance of different in-stream habitats to POM generation and export on daily to seasonal timescales, with implications for biogeochemical cycling and the local diatom metacommunity.

Bacteria and diatom co-occurrence patterns in microbial mats from polar desert streams.

The ephemeral stream habitats of the McMurdo Dry Valleys of Antarctica support desiccation and freeze-tolerant microbial mats that are hot spots of primary productivity in an otherwise inhospitable environment. The ecological processes that structure bacterial communities in this harsh environment are not known; however, insights from diatom community ecology may prove to be informative. We examined the relationships between diatoms and bacteria at the community and taxon levels. The diversity and community structure of stream microbial mats were characterized using high-throughput pyrosequencing for bacteria and morphological identification for diatoms. We found significant relationships between diatom communities and the communities of cyanobacteria and heterotrophic bacteria, and co-occurrence analysis identified numerous correlations between the relative abundances of individual diatom and bacterial taxa, which may result from species interactions. Additionally, the strength of correlations between heterotrophic bacteria and diatoms varied along a hydrologic gradient, indicating that flow regime may influence the overall community structure. Phylogenetic consistency in the co-occurrence patterns suggests that the associations are ecologically relevant. Despite these community- and taxon-level relationships, diatom and bacterial alpha diversity were inversely correlated, which may highlight a fundamental difference between the processes that influence bacterial and diatom community assembly in these streams. Our results therefore demonstrate that the relationships between diatoms and bacteria are complex and may result from species interactions as well as niche-specific processes.

L- and N-current but not M-current inhibition by M1 muscarinic receptors requires DAG lipase activity.

Stimulation of postsynaptic M(1) muscarinic receptors (M(1)Rs) increases firing rates of both sympathetic and central neurons that underlie increases in vasomotor tone, heart rate, and cognitive memory functioning. At the cellular level, M(1)R stimulation modulates currents through various voltage-gated ion channels, including KCNQ K+ channels (M-current) and both L- and N-type Ca2+ channels (L- and N-current) by a pertussis toxin-insensitive, slow signaling pathway. Depletion of phosphatidylinositol-4,5-bisphosphate (PIP2) during M(1)R stimulation suffices to inhibit M-current. We found previously that following PIP2 hydrolysis by phospholipase C, activation of phospholipase A2 and liberation of a lipid metabolite, most likely arachidonic acid (AA) are necessary for L- and N-current modulation. Here we examined the involvement of a third lipase, diacylglycerol lipase (DAGL), in the slow pathway. We documented the presence of DAGL in superior cervical ganglion neurons, and then tested the highly selective DAGL inhibitor, RHC-80267, for its capacity to antagonize M(1)R-mediated modulation of whole-cell Ca2+ currents. RHC-80267 significantly reduced L- and N-current inhibition by the muscarinic agonist oxotremorine-M (Oxo-M) but did not affect their inhibition by exogenous AA. Moreover, voltage-dependent inhibition of N-current by Oxo-M remained in the presence of RHC-80267, indicating selective action on the slow pathway. RHC also blocked inhibition of recombinant N-current. In contrast, RHC-80267 had no effect on native M-current inhibition. These data are consistent with a role for DAGL in mediating L- and N-current inhibition. These results extend our previous findings that the signaling pathway mediating L- and N-current inhibition diverges from the pathway initiating M-current inhibition.

Diversity patterns of microbial eukaryotes mirror those of bacteria in Antarctic cryoconite holes.

Ice-lidded cryoconite holes on glaciers in the Taylor Valley, Antarctica, provide a unique system of natural mesocosms for studying community structure and assembly. We used high-throughput DNA sequencing to characterize both microbial eukaryotic communities and bacterial communities within cryoconite holes across three glaciers to study similarities in their spatial patterns. We expected that the alpha (phylogenetic diversity) and beta (pairwise community dissimilarity) diversity patterns of eukaryotes in cryoconite holes would be related to those of bacteria, and that they would be related to the biogeochemical gradient within the Taylor Valley. We found that eukaryotic alpha and beta diversity were strongly related to those of bacteria across scales ranging from 140 m to 41 km apart. Alpha diversity of both was significantly related to position in the valley and surface area of the cryoconite hole, with pH also significantly correlated with the eukaryotic diversity. Beta diversity for both bacteria and eukaryotes was significantly related to position in the valley, with bacterial beta diversity also related to nitrate. These results are consistent with transport of sediments onto glaciers occurring primarily at local scales relative to the size of the valley, thus creating feedbacks in local chemistry and diversity.

M1 muscarinic receptors inhibit L-type Ca2+ current and M-current by divergent signal transduction cascades.

Ion channels reside in a sea of phospholipids. During normal fluctuations in membrane potential and periods of modulation, lipids that directly associate with channel proteins influence gating by incompletely understood mechanisms. In one model, M(1)-muscarinic receptors (M(1)Rs) may inhibit both Ca(2+) (L- and N-) and K(+) (M-) currents by losing a putative interaction between channels and phosphatidylinositol-4,5-bisphosphate (PIP(2)). However, we found previously that M(1)R inhibition of N-current in superior cervical ganglion (SCG) neurons requires loss of PIP(2) and generation of a free fatty acid, probably arachidonic acid (AA) by phospholipase A(2) (PLA(2)). It is not known whether PLA(2) activity and AA also participate in L- and M-current modulation in SCG neurons. To test whether PLA(2) plays a similar role in M(1)R inhibition of L- and M-currents, we used several experimental approaches and found unanticipated divergent signaling. First, blocking resynthesis of PIP(2) minimized M-current recovery from inhibition, whereas L-current recovered normally. Second, L-current inhibition required group IVa PLA(2) [cytoplasmic PLA(2) (cPLA(2))], whereas M-current did not. Western blot and imaging studies confirmed acute activation of cPLA(2) by muscarinic stimulation. Third, in type IIa PLA(2) [secreted (sPLA(2))](-/-)/cPLA(2)(-/-) double-knock-out SCG neurons, muscarinic inhibition of L-current decreased. In contrast, M-current inhibition remained unaffected but recovery was impaired. Our results indicate that L-current is inhibited by a pathway previously shown to control M-current over-recovery after washout of muscarinic agonist. Our findings support a model of M(1)R-meditated channel modulation that broadens rather than restricts the roles of phospholipids and fatty acids in regulating ion channel activity.

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA.

The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria), MLE1-12 (phylum Cyanobacteria), Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources.

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.

Molecular analysis of single room humidifier bacteriology.

Portable, single-room humidifiers are commonly used in homes for comfort and health benefits, but also create habitats for microbiology. Currently there is no information on home humidifier microbiology aside from anecdotal evidence of infection with opportunistic pathogens and irritation from endotoxin exposure. To obtain a broader perspective on humidifier microbiology, DNAs were isolated from tap source waters, tank waters, and biofilm samples associated with 26 humidifiers of ultrasonic and boiling modes of operation in the Front Range of Colorado. Humidifiers sampled included units operated by individuals in their homes, display models continuously operated by a retail store, and new humidifiers operated in a controlled laboratory study. The V1V2 region of the rRNA gene was amplified and sequenced to determine the taxonomic composition of humidifier samples. Communities encountered were generally low in richness and diversity and were dominated by Sphingomonadales, Rhizobiales, and Burkholderiales of the Proteobacteria, and MLE1-12, a presumably non-photosynthetic representative of the cyanobacterial phylum. Very few sequences of potential health concern were detected. The bacteriology encountered in source waters sampled here was similar to that encountered in previous studies of municipal drinking waters. Source water bacteriology was found to have the greatest effect on tank water and biofilm bacteriology, an effect confirmed by a controlled study comparing ultrasonic and boiler humidifiers fed with tap vs. treated (deionized, reverse osmosis, 0.2 µm filtered) water over a period of two months.

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes.

Soil microbial communities play a critical role in nutrient transformation and storage in all ecosystems. Quantifying the seasonal and long-term temporal extent of genetic and functional variation of soil microorganisms in response to biotic and abiotic changes within and across ecosystems will inform our understanding of the effect of climate change on these processes. We examined spatial and seasonal variation in microbial communities based on 16S rRNA gene sequencing and phospholipid fatty acid (PLFA) composition across four biomes: a tropical broadleaf forest (Hawaii), taiga (Alaska), semiarid grassland-shrubland (Utah), and a subtropical coniferous forest (Florida). In this study, we used a team-based instructional approach leveraging the iPlant Collaborative to examine publicly available National Ecological Observatory Network (NEON) 16S gene and PLFA measurements that quantify microbial diversity, composition, and growth. Both profiling techniques revealed that microbial communities grouped strongly by ecosystem and were predominately influenced by three edaphic factors: pH, soil water content, and cation exchange capacity. Temporal variability of microbial communities differed by profiling technique; 16S-based community measurements showed significant temporal variability only in the subtropical coniferous forest communities, specifically through changes within subgroups of Acidobacteria. Conversely, PLFA-based community measurements showed seasonal shifts in taiga and tropical broadleaf forest systems. These differences may be due to the premise that 16S-based measurements are predominantly influenced by large shifts in the abiotic soil environment, while PLFA-based analyses reflect the metabolically active fraction of the microbial community, which is more sensitive to local disturbances and biotic interactions. To address the technical issue of the response of soil microbial communities to sample storage temperature, we compared 16S-based community structure in soils stored at -80°C and -20°C and found no significant differences in community composition based on storage temperature. Free, open access datasets and data sharing platforms are powerful tools for integrating research and teaching in undergraduate and graduate student classrooms. They are a valuable resource for fostering interdisciplinary collaborations, testing ecological theory, model development and validation, and generating novel hypotheses. Training in data analysis and interpretation of large datasets in university classrooms through project-based learning improves the learning experience for students and enables their use of these significant resources throughout their careers.

Patterns and processes of microbial community assembly.

Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183-206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.

The Ca2+ channel beta subunit determines whether stimulation of Gq-coupled receptors enhances or inhibits N current.

In superior cervical ganglion (SCG) neurons, stimulation of M(1) receptors (M(1)Rs) produces a distinct pattern of modulation of N-type calcium (N-) channel activity, enhancing currents elicited with negative test potentials and inhibiting currents elicited with positive test potentials. Exogenously applied arachidonic acid (AA) reproduces this profile of modulation, suggesting AA functions as a downstream messenger of M(1)Rs. In addition, techniques that diminish AA's concentration during M(1)R stimulation minimize N-current modulation. However, other studies suggest depletion of phosphatidylinositol-4,5-bisphosphate during M(1)R stimulation suffices to elicit modulation. In this study, we used an expression system to examine the physiological mechanisms regulating modulation. We found the beta subunit (Ca(V)beta) acts as a molecular switch regulating whether modulation results in enhancement or inhibition. In human embryonic kidney 293 cells, stimulation of M(1)Rs or neurokinin-1 receptors (NK-1Rs) inhibited activity of N channels formed by Ca(V)2.2 and coexpressed with Ca(V)beta1b, Ca(V)beta3, or Ca(V)beta4 but enhanced activity of N channels containing Ca(V)beta2a. Exogenously applied AA produced the same pattern of modulation. Coexpression of Ca(V)beta2a, Ca(V)beta3, and Ca(V)beta4 recapitulated the modulatory response previously seen in SCG neurons, implying heterogeneous association of Ca(V)beta with Ca(V)2.2. Further experiments with mutated, chimeric Ca(V)beta subunits and free palmitic acid revealed that palmitoylation of Ca(V)beta2a is essential for loss of inhibition. The data presented here fit a model in which Ca(V)beta2a blocks inhibition, thus unmasking enhancement. Our discovery that the presence or absence of palmitoylated Ca(V)beta2a toggles M(1)R- or NK-1R-mediated modulation of N current between enhancement and inhibition identifies a novel role for palmitoylation. Moreover, these findings predict that at synapses, modulation of N-channel activity by M(1)Rs or NK-1Rs will fluctuate between enhancement and inhibition based on the presence of palmitoylated Ca(V)beta2a.