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USGS2021

Nutrients and warming alter mountain lake benthic algal structure and function

In recent years, benthic algae have been increasing in abundance in the littoral zones of oligotrophic lakes, but causality has been hard to assign. We used field and laboratory experiments to explore the implications of increasing water temperature and nutrient availability for benthic algal assemblages and ecosystem processes in a Colorado alpine lake. We tested the effect of nutrient enrichment on the relative abundance of algal taxonomic groups in situ using nutrient diffusing substrata. We manipulated temperature and nutrient concentrations in laboratory assays to assess their interactive effects on ecosystem function of chlorophyte-dominated benthic assemblages. Nutrient enrichment with both N and P favored Chlorophyta (green algae) in field experiments and produced the highest overall algal biomass. In the absence of nutrient enrichment, the relative abundance of Bacillariophyta (diatoms) was substantially greater than that of Chlorophyta and cyanobacteria. In laboratory assays, N uptake increased but net ecosystem production decreased with warming temperatures, resulting in reduced N-use efficiency. Even though dissolved organic C (DOC) substantially increased in solution after all laboratory incubations, lower DOC concentrations in the assays with added P and warmer temperatures suggest nutrients and warming stimulated heterotrophic microorganisms as well as primary producers. Our results demonstrate that nutrient availability stimulates Chlorophyta in benthic algal assemblages and that the increase in chlorophytes may alter ecosystem processes with ongoing, rapid environmental change, including N cycling and metabolic functions in oligotrophic lake littoral habitats.

Freshwater Science↗

USGS2019

Microbial Fe(II) oxidation by Sideroxydans lithotrophicus ES-1 in the presence of Schlöppnerbrunnen fen derived humic acids

Controlled laboratory experiments were combined with field measurements to better understand the interactions between dissolved organic matter (DOM) and reduced iron in organic-rich peatlands. Addition of peat-derived humic acid extract (HA) to Sideroxydans lithotrophicus ES-1 liquid cultures led to higher cell numbers and up to 1.4 times higher Fe(II) oxidation rates compared to chemical controls. This effect was positively correlated with increasing HA concentrations. Similar Fe(III) (oxyhydr)oxide mineralogies were formed both abiotically and biotically irrespective of HA amendment, but minerals formed in the presence of ES-1 and HA were smaller. ES-1 growth with HA promoted aggregation of Fe(III) products in agarose-stabilized gradient tubes as shown by voltammetric profiling. In situ voltammetry in an acidic, iron-rich peatland revealed a gap between oxygen penetration and iron reduction that may reflect active Fe(II)-oxidizing microorganisms. The highest abundance of Fe(II) oxidizers Sideroxydans (4.9 x 107 gene copies gww-1) and Gallionella (1.5 x 107 gene copies gww-1) in the upper peat layer coincided with small-sized minerals resembling nanoparticulate ferrihydrite or goethite. Our results suggest that microbially-mediated Fe(II) oxidation dominates in the presence of DOM leading to the formation of nano-sized biogenic Fe(III) (oxyhydr)oxides that might be are readily bioavailable and likely important to iron and carbon cycling.

FEMS Microbiology Ecology↗

USGS2020

Mapping metabolic activity at single cell resolution in intact volcanic fumarole soil

Interactions among microorganisms and their mineralogical substrates govern the structure, function, and emergent properties of microbial communities. These interactions are predicated on spatial relationships, which dictate metabolite exchange and access to key substrates. To quantitatively assess links between spatial relationships and metabolic activity, this study presents a novel approach to map all organisms, the metabolically active subset, and associated mineral grains, all while maintaining spatial integrity of an environmental microbiome. We applied this method at an outgassing fumarole of Vanuatu’s Marum Crater, one of the largest point sources of several environmentally relevant gaseous compounds, including H2O, CO2, and SO2. With increasing distance from the soil-air surface and from mineral grain outer boundaries, organism abundance decreased but the proportion of metabolically active organisms often increased. These protected niches may provide more stable conditions that promote consistent metabolic activity of a streamlined community. Conversely, mineral exteriors accumulate more organisms that may cover a wider range of preferred conditions, implying that only a subset of the community will be active under any particular environmental regime. More broadly, the approach presented here allows investigators to see microbial communities “as they really are” and explore determinants of metabolic activity across a range of microbiomes.

FEMS Microbiology Letters↗

USGS2017

Autotrophic microbial arsenotrophy in arsenic-rich soda lakes

A number of prokaryotes are capable of employing arsenic oxy-anions as either electron acceptors [arsenate; As(V)] or electron donors [arsenite; As(III)] to sustain arsenic-dependent growth (‘arsenotrophy’). A subset of these microorganisms function as either chemoautotrophs or photoautotrophs, whereby they gain sufficient energy from their redox metabolism of arsenic to completely satisfy their carbon needs for growth by autotrophy, that is the fixation of inorganic carbon (e.g. HCO 3 − ) into their biomass. Here we review what has been learned of these processes by investigations we have undertaken in three soda lakes of the western USA and from the physiological characterizations of the relevant bacteria, which include the critical genes involved, such as respiratory arsenate reductase ( arrA ) and the discovery of its arsenite-oxidizing counterpart ( arxA ). When possible, we refer to instances of similar process occurring in other, less extreme ecosystems and by microbes other than haloalkaliphiles.

FEMS Microbiology Letters↗

USGS2022

Great diversity of KSα sequences from bat-associated microbiota suggests novel sources of uncharacterized natural products

Polyketide synthases (PKSs) are multidomain enzymes in microorganisms that synthesize complex, bioactive molecules. PKS II systems are iterative, containing only a single representative of each domain: ketosynthase alpha (KS α "> α � ⁠ ), ketosynthase beta and the acyl carrier protein. Any gene encoding for one of these domains is representative of an entire PKS II biosynthetic gene cluster (BGC). Bat skin surfaces represent an extreme environment prolific in Actinobacteria that may constitute a source for bioactive molecule discovery. KS α "> α � sequences were obtained from culturable bacteria from bats in the southwestern United States. From 467 bat bacterial isolates, we detected 215 (46%) had KS α "> α � sequences. Sequencing yielded 210 operational taxonomic units, and phylogenetic placement found 45 (21%) shared <85% homology to characterized metabolites. Additionally, 16 Actinobacteria genomes from the bat microbiome were analyzed for biosynthetic capacity. A range of 69–93% of the BGCs were novel suggesting the bat microbiome may contain valuable uncharacterized natural products. Documenting and characterizing these are important in understanding the susceptibility of bats to emerging infectious diseases, such as white-nose syndrome. Also noteworthy was the relationship between KS α "> α � homology and total BGC novelty within each fully sequenced strain. We propose amplification and detection of KS α "> α � could predict a strain's global biosynthetic capacity.

FEMS Microbiology Ecology↗

USGS2026

Deep subsurface organic-rich shale supports abundant, diverse, and novel fungi

As Earth’s principal reservoir of organic carbon and microbial biomass, the deep subsurface hosts microorganisms capable of mobilizing this once-sequestered carbon. Contrary to standard assumptions of eukaryotic scarcity, this study documents abundant fungal communities, ranging from 4.2 × 10 3 to 6.8 × 10 3 fungal cells mL −1 , across a methane-producing organic-rich shale 247–556 meters below the surface. Although fungal:bacterial cell ratios ranged from 1:7028 to 1:713, application of biomass conversion factors developed for oceanic systems yielded a median fungal:bacterial biomass ratio of 1:4.7. 16S rRNA gene amplicons revealed bacterial and archaeal communities mirroring those found in well-characterized extremophilic, carbon-degrading environments, while sequencing of 18S rRNA gene and ITS rRNA spacer amplicons collectively identified a eukaryotic hotspot with 689 fungal OTUs across six phyla. The dominant fungal classes, Agaricomycetes and Dothideomycetes, are well-established degraders of recalcitrant carbon compounds at the surface, suggesting they may similarly contribute to organic matter degradation and ecosystem maintenance in the subsurface. Cultivation and isolation efforts yielded 205 fungal strains, including 13 candidate novel taxa, underscoring the deep subsurface as an underexplored eukaryotic habitat. Stable carbon isotopes indicate methane is predominantly generated via microbial conversion of the fossil carbon, while water isotopes suggest in situ geochemical conditions have been relatively stable since the Late Pleistocene, with subglacial recharge as a plausible mechanism for microbial introduction. Collectively, these findings suggest that fungi are underrecognized contributors to organic matter transformation and functional diversity in the deep biosphere, revealing a critical gap in our understanding of deep subsurface ecosystem processes.

Indiana, Michigan, Ohio↗

USGS2019

Manipulating wild and tamed phytobiomes: Challenges and opportunities

This white paper presents a series of perspectives on current and future phytobiome management, discussed at the Wild and Tamed Phytobiomes Symposium in University Park, PA, USA, in June 2018. To enhance plant productivity and health, and to translate lab- and greenhouse-based phytobiome research to field applications, the academic community and end-users need to address a variety of scientific, practical, and social challenges. Prior discussion of phytobiomes has focused heavily on plant-associated bacterial and fungal assemblages, but the phytobiomes concept covers all factors that influence plant function. Here we discuss various management considerations, including abiotic conditions (e.g. soil, nutrient applications), microorganisms (e.g. bacterial and fungal assemblages, bacterial and fungal inoculants, viruses), macroorganisms (e.g. arthropods, plant genetics), and societal factors (e.g. communication approaches, technology diffusion). An important near-term goal for this field should be to estimate the potential relative contribution of different components of the phytobiome to plant health, as well as the potential and risk of modifying each in the near-future.

Phytobiomes Journal↗

USGS2016

Body size distributions signal a regime shift in a lake ecosystem

Communities of organisms, from mammals to microorganisms, have discontinuous distributions of body size. This pattern of size structuring is a conservative trait of community organization and is a product of processes that occur at multiple spatial and temporal scales. In this study, we assessed whether body size patterns serve as an indicator of a threshold between alternative regimes. Over the past 7000 years, the biological communities of Foy Lake (Montana, USA) have undergone a major regime shift owing to climate change. We used a palaeoecological record of diatom communities to estimate diatom sizes, and then analysed the discontinuous distribution of organism sizes over time. We used Bayesian classification and regression tree models to determine that all time intervals exhibited aggregations of sizes separated by gaps in the distribution and found a significant change in diatom body size distributions approximately 150 years before the identified ecosystem regime shift. We suggest that discontinuity analysis is a useful addition to the suite of tools for the detection of early warning signals of regime shifts.

Proceedings of the Royal Society B↗

USGS2015

Concentration and retention of Toxoplasma gondii oocysts by marine snails demonstrate a novel mechanism for transmission of terrestrial zoonotic pathogens in coastal ecosystems

The parasite T oxoplasma gondii is an environmentally persistent pathogen that can cause fatal disease in humans, terrestrial warm-blooded animals and aquatic mammals. Although an association between T . gondii exposure and prey specialization on marine snails was identified in threatened California sea otters, the ability of kelp-dwelling snails to transmit terrestrially derived pathogens has not been previously investigated. The objective of this study was to measure concentration and retention of T . gondii by marine snails in laboratory aquaria, and to test for natural T . gondii contamination in field-collected snails. Following exposure to T . gondii -containing seawater, oocysts were detected by microscopy in snail faeces and tissues for 10 and 3 days respectively. Nested polymerase chain reaction was also applied as a method for confirming putative T . gondii oocysts detected in snail faeces and tissues by microscopy. T oxoplasma gondii was not detected in field-collected snails. Results suggest that turban snails are competent transport hosts for T . gondii . By concentrating oocysts in faecal pellets, snails may facilitate entry of T . gondii into the nearshore marine food web. This novel mechanism also represents a general pathway by which marine transmission of terrestrially derived microorganisms can be mediated via pathogen concentration and retention by benthic invertebrates.

Environmental Microbiology↗

USGS2012

Comparison of DNA preservation methods for environmental bacterial community samples

Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote locations is common, and preservation of microbial community DNA for later study is critical. A particular challenge is keeping samples frozen in transit. Five nucleic acid preservation methods that do not require cold storage were compared for effectiveness over time and ease of use. Mixed microbial communities of known composition were created and preserved by DNAgard™, RNAlater ® , DMSO–EDTA–salt (DESS), FTA ® cards, and FTA Elute ® cards. Automated ribosomal intergenic spacer analysis and clone libraries were used to detect specific changes in the faux communities over weeks and months of storage. A previously known bias in FTA ® cards that results in lower recovery of pure cultures of Gram-positive bacteria was also detected in mixed community samples. There appears to be a uniform bias across all five preservation methods against microorganisms with high G + C DNA. Overall, the liquid-based preservatives (DNAgard™, RNAlater ® , and DESS) outperformed the card-based methods. No single liquid method clearly outperformed the others, leaving method choice to be based on experimental design, field facilities, shipping constraints, and allowable cost.

FEMS Microbiology Ecology↗

USGS2013

Microbial community composition and endolith colonization at an Arctic thermal spring are driven by calcite precipitation

Environmental conditions shape community composition. Arctic thermal springs provide an opportunity to study how environmental gradients can impose strong selective pressures on microbial communities and provide a continuum of niche opportunities. We use microscopic and molecular methods to conduct a survey of microbial community composition at Troll Springs on Svalbard, Norway, in the high Arctic. Microorganisms there exist under a wide range of environmental conditions: in warm water as periphyton, in moist granular materials, and in cold, dry rock as endoliths. Troll Springs has two distinct ecosystems, aquatic and terrestrial, together in close proximity, with different underlying environmental factors shaping each microbial community. Periphyton are entrapped during precipitation of calcium carbonate from the spring's waters, providing microbial populations that serve as precursors for the development of endolithic communities. This process differs from most endolith colonization, in which the rock predates the communities that colonize it. Community composition is modulated as environmental conditions change within the springs. At Troll, the aquatic environments show a small number of dominant operational taxonomic units (OTUs) that are specific to each sample. The terrestrial environments show a more even distribution of OTUs common to multiple samples.

Environmental Microbiology Reports↗

USGS2019

The importance of groundwater flow to the formation of modern thrombolitic microbialites

Modern microbialites are often located within groundwater discharge zones, yet the role of groundwater in microbialite accretion has yet to be resolved. To understand relationships between groundwater, microbialites, and associated microbial communities, we quantified and characterized groundwater flow and chemistry in active thrombolitic microbialites in Lake Clifton, Western Australia, and compared these observations to inactive thrombolites and lakebed sediments. Groundwater flows upward through an interconnected network of pores within the microstructure of active thrombolites, discharging directly from thrombolite heads into the lake. This upwelling groundwater is fresher than lake water and is hypothesized to support microbial mat growth by reducing salinity and providing limiting nutrients in an osmotically stressful and oligotrophic habitat. This is in contrast to inactive thrombolites that show no evidence of microbial mat colonization and are infiltrated by hypersaline lake water. Groundwater discharge through active thrombolites contrasts with the surrounding lakebed, where hypersaline lake water flows downward through sandy sediments at very low rates. Based on an appreciation for the role of microorganisms in thrombolite accretion, our findings suggest conditions favorable to thrombolite formation still exist in certain locations of Lake Clifton despite increasing lake water salinity. This study is the first to characterize groundwater flow rates, paths, and chemistry within a microbialite‐forming environment and provides new insight into how groundwater can support microbial mats believed to contribute to microbialite formation in modern and ancient environments.

Geobiology↗

USGS2011

Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge

To evaluate the effects of local fluid geochemistry on microbial communities associated with active hydrothermal vent deposits, we examined the archaeal and bacterial communities of 12 samples collected from two very different vent fields: the basalt-hosted Lucky Strike (37°17'N, 32°16.3'W, depth 1600-1750m) and the ultramafic-hosted Rainbow (36°13'N, 33°54.1'W, depth 2270-2330m) vent fields along the Mid-Atlantic Ridge (MAR). Using multiplexed barcoded pyrosequencing of the variable region 4 (V4) of the 16S rRNA genes, we show statistically significant differences between the archaeal and bacterial communities associated with the different vent fields. Quantitative polymerase chain reaction (qPCR) assays of the functional gene diagnostic for methanogenesis ( mcr A), as well as geochemical modelling to predict pore fluid chemistries within the deposits, support the pyrosequencing observations. Collectively, these results show that the less reduced, hydrogen-poor fluids at Lucky Strike limit colonization by strict anaerobes such as methanogens, and allow for hyperthermophilic microaerophiles, like Aeropyrum . In contrast, the hydrogen-rich reducing vent fluids at the ultramafic-influenced Rainbow vent field support the prevalence of methanogens and other hydrogen-oxidizing thermophiles at this site. These results demonstrate that biogeographical patterns of hydrothermal vent microorganisms are shaped in part by large scale geological and geochemical processes.

Environmental Microbiology↗

USGS2005

Microbial H2 cycling does not affect δ2H values of ground water

Stable hydrogen-isotope values of ground water (δ 2 H) and dissolved hydrogen concentrations (H (2(aq) ) were quantified in a petroleum-hydrocarbon contaminated aquifer to determine whether the production/consumption of H 2 by subsurface microorganisms affects ground water &delta 2 H values. The range of &delta 2 H observed in monitoring wells sampled (-27.8 &permil; c to -15.5 &permil; c ) was best explained, however, by seasonal differences in recharge temperature as indicated using ground water δ 18 O values, rather than isotopic exchange reactions involving the microbial cycling of H 2 during anaerobic petroleum-hydrocarbon biodegradation. The absence of a measurable hydrogen-isotope exchange between microbially cycled H 2 and ground water reflects the fact that the amount of H 2 available from the anaerobic decomposition of petroleum hydrocarbons is small relative to the amount of hydrogen present in water, even though milligram per liter concentrations of readily biodegradable contaminants are present at the study site. Additionally, isotopic fractionation calculations indicate that in order for H 2 cycling processes to affect δ 2 H values of ground water, relatively high concentrations of H 2 (>0.080 M) would have to be maintained, considerably higher than the 0.2 to 26 nM present at this site and characteristic of anaerobic conditions in general. These observations suggest that the conventional approach of using δ 2 H and δ 18 O values to determine recharge history is appropriate even for those ground water systems characterized by anaerobic conditions and extensive microbial H 2 cycling.

Ground Water↗

USGS2009

Distinguishing iron-reducing from sulfate-reducing conditions

Ground water systems dominated by iron‐ or sulfate‐reducing conditions may be distinguished by observing concentrations of dissolved iron (Fe 2+ ) and sulfide (sum of H 2 S, HS − , and S = species and denoted here as “H 2 S”). This approach is based on the observation that concentrations of Fe 2+ and H 2 S in ground water systems tend to be inversely related according to a hyperbolic function. That is, when Fe 2+ concentrations are high, H 2 S concentrations tend to be low and vice versa. This relation partly reflects the rapid reaction kinetics of Fe 2+ with H 2 S to produce relatively insoluble ferrous sulfides (FeS). This relation also reflects competition for organic substrates between the iron‐ and the sulfate‐reducing microorganisms that catalyze the production of Fe 2+ and H 2 S. These solubility and microbial constraints operate in tandem, resulting in the observed hyperbolic relation between Fe 2+ and H 2 S concentrations. Concentrations of redox indicators, including dissolved hydrogen (H 2 ) measured in a shallow aquifer in Hanahan, South Carolina, suggest that if the Fe 2+ /H 2 S mass ratio (units of mg/L) exceeded 10, the screened interval being tapped was consistently iron reducing (H 2 ∼0.2 to 0.8 nM). Conversely, if the Fe 2+ /H 2 S ratio was less than 0.30, consistent sulfate‐reducing (H 2 ∼1 to 5 nM) conditions were observed over time. Concomitantly high Fe 2+ and H 2 S concentrations were associated with H 2 concentrations that varied between 0.2 and 5.0 nM over time, suggesting mixing of water from adjacent iron‐ and sulfate‐reducing zones or concomitant iron and sulfate reduction under nonelectron donor–limited conditions. These observations suggest that Fe 2+ /H 2 S mass ratios may provide useful information concerning the occurrence and distribution of iron and sulfate reduction in ground water systems.

Ground Water↗

USGS2005

Behavior of a chlorinated ethene plume following source-area treatment with Fenton's reagent

Monitoring data collected over a 6‐year period show that a plume of chlorinated ethene–contaminated ground water has contracted significantly following treatment of the contaminant source area using in situ oxidation. Prior to treatment (1998), concentrations of perchloroethene (PCE) exceeded 4500 μg/L in a contaminant source area associated with a municipal landfill in Kings Bay, Georgia. The plume emanating from this source area was characterized by vinyl chloride (VC) concentrations exceeding 800 μg/L. In situ oxidation using Fenton's reagent lowered PCE concentrations in the source area below 100 μg/L, and PCE concentrations have not rebounded above this level since treatment. In the 6 years following treatment, VC concentrations in the plume have decreased significantly. These concentration declines can be attributed to the movement of Fenton's reagent–treated water downgradient through the system, the cessation of a previously installed pump‐and‐treat system, and the significant natural attenuation capacity of this anoxic aquifer. While in situ oxidation briefly decreased the abundance and activity of microorganisms in the source area, this activity rebounded in <6 months. Nevertheless, the shift from sulfate‐reducing to Fe(III)‐reducing conditions induced by Fenton's treatment may have decreased the efficiency of reductive dechlorination in the injection zone. The results of this study indicate that source‐area removal actions, particularly when applied to ground water systems that have significant natural attenuation capacity, can be effective in decreasing the areal extent and contaminant concentrations of chlorinated ethene plumes.

Ground Water Monitoring and Remediation↗

USGS2006

Effect of H2 and redox condition on biotic and abiotic MTBE transformation

Laboratory studies conducted with surface water sediment from a methyl tert-butyl ether (MTBE)-contaminated site in South Carolina demonstrated that, under methanogenic conditions, [U-14C] MTBE was transformed to 14C tert-butyl alcohol (TBA) with no measurable production of 14CO2. Production of TBA was not attributed to the activity of methanogenic microorganisms, however, because comparable transformation of [U-14C] MTBE to 14C-TBA also was observed in heat-sterilized controls with dissolved H2 concentrations > 5 nM. The results suggest that the transformation of MTBE to TBA may be an abiotic process that is driven by biologically produced H2 under in situ conditions. In contrast, mineralization of [U-14C] MTBE to 14CO2 was completely inhibited by heat sterilization and only observed in treatments characterized by dissolved H2 concentrations < 2 nM. These results suggest that the pathway of MTBE transformation is influenced by in situ H2 concentrations and that in situ H2 concentrations may be an useful indicator of MTBE transformation pathways in ground water systems.

Ground Water Monitoring and Remediation↗

USGS2016

Natural inactivation of Escherichia coli in anoxic and reduced groundwater

Aims Inactivation rates of E. coli in groundwater have most often been determined in aerobic and oxidized systems. This study examined E. coli inactivation rates in anaerobic and extremely reduced groundwater systems that have been identified as recharge zones. Methods and Results Groundwater from six artesian wells was diverted to above ground, flow through mesocosms that contained laboratory grown E. coli in diffusion chambers. All groundwater was anaerobic and extremely reduced (ORP < - 300 mV). Cells were plated onto mTEC agar during 21 day incubation periods. All data fit a bi-phasic inactivation model, with > 95% of the E. coli population being inactivated < 11.0 hrs (mean k = 0.488± 0.188 h −1 ). Conclusions The groundwater geochemical conditions enhanced the inactivation of E. coli to rates approximately 21-fold greater than previously published inactivation rate in groundwater (mean k = 0.023 ± 0.030 h −1 ). Also, mTEC agar inhibits E. coli growth following exposure to anaerobic and reduced groundwater. Significance and Impact of the Study Aquifer recharge zones with geochemical characteristics observed in this study complement above ground engineered processes (e.g., filtration, disinfection), while increasing the overall indicator microorganism log-reduction rate of a facility.

Journal of Applied Microbiology↗