Microbial Biogeochemistry Research Articles

The influence of river basin nitrogen pollution sources and their transport on microbial community structure

The characterization of variations in riverine microbiota that stem from contaminant sources and transport modes is important for understanding biogeochemical processes. However, the association between complex anthropogenic nitrogen pollution and bacteria has not been extensively investigated owing to the difficulties faced while determining the distribution of nitrogen contaminants in watersheds. Here, we employed the Nitrogen and Oxygen Stable Isotope Tools alongside microbiological analysis to explore microbial characteristics and their responses to complex nitrogen pollution patterns. Significant changes in microbial communities were observed in watersheds with different complex nitrogen pollution sources migrating. Complex nitrogen sources were closely associated with microbiota. The main sources of nitrogen pollution in the dry season watershed were Manurc and Sewage (M&S, 54.2%). M&S exhibited reduced microbial diversity, high number of denitrification groups, and increased nitrogen cycling compared with others. However, Soil Nitrogen sources (SN, 59.3%) in the watershed during the wet season were the main contributors of nitrogen in the watershed. Eluviation allows SN to increased microbial community similarity, in addition to facilitating microbial immobilization processes. Overall, this study expands our knowledge regarding microbial biogeochemistry in catchments and beyond by linking specific nitrogen pollution scenarios to microorganisms.

Deciphering Microbial Communities and Distinct Metabolic Pathways in the Tangyin Hydrothermal Fields of Okinawa Trough through Metagenomic and Genomic Analyses.

Deep-sea hydrothermal vents have been extensively explored around the globe in the past decades, and the diversity of microbial communities and their ecological functions related to hydrothermal vents have become hotspots in the study of microbial biogeochemistry. However, knowledge of dominant microbial communities and their unique metabolic characteristics adapting to hydrothermal vents is still limited. In our study, the sediment sample near the Tangyin hydrothermal vent in the southern part of the Okinawa Trough was collected, and the most abundant phyla are Proteobacteria and Desulfobacterota based on the 16S rRNA genes and metagenome sequencing. Metagenomic analysis revealed that methane metabolism, sulfur reduction, and Fe2+ uptake were abundantly distributed in hydrothermal sediment. In addition, most of the metagenomic assembly genomes (MAGs), belonging to Chloroflexota, Desulfobacterota, and Gammaproteobacteria, were found to be involved in methanogenesis, sulfur oxidation/reduction, and ferrous/ferric iron metabolisms. Among these MAGs, the two representative groups (Bathyarchaeia and Thioglobaceae) also showed distinct metabolic characteristics related to carbon, sulfur, and iron to adapt to hydrothermal environments. Our results reveal the dominant microbial populations and their metabolic features in the sediment near the Tangyin hydrothermal fields, providing a better understanding of microbial survival strategies in the extreme environment.

The Dawn of the BioGeoSCAPES Program: Ocean Metabolism and Nutrient Cycles on a Changing Planet

Biogeochemical cycles constitute Earth’s life support system and distinguish our planet from others in this solar system. Microorganisms are the primary drivers of these cycles. Understanding the controls on marine microbial dynamics and how microbes will respond to environmental change is essential for building and assessing model-based forecasts and generating robust projections of climate change impacts on ocean productivity and biogeochemical cycles. An international community effort has been underway to create a global-scale marine microbial biogeochemistry research program to tackle gaps in this understanding. The BioGeoSCAPES: Ocean Metabolism and Nutrient Cycles on a Changing Planet program will identify and quantify how marine microbes adjust to a changing climate and assess the consequences for global biogeochemical cycles. This article summarizes the ongoing efforts to launch BioGeoSCAPES.

Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil's Hole, Bermuda.

Oxygen minimum zones (OMZs) are expanding due to increased sea surface temperatures, subsequent increased oxygen demand through respiration, reduced oxygen solubility, and thermal stratification driven in part by anthropogenic climate change. Devil's Hole, Bermuda is a model ecosystem to study OMZ microbial biogeochemistry because the formation and subsequent overturn of the suboxic zone occur annually. During thermally driven stratification, suboxic conditions develop, with organic matter and nutrients accumulating at depth. In this study, the bioavailability of the accumulated dissolved organic carbon (DOC) and the microbial community response to reoxygenation of suboxic waters was assessed using a simulated overturn experiment. The surface inoculated prokaryotic community responded to the deep (formerly suboxic) 0.2 μm filtrate with cell densities increasing 2.5-fold over 6 days while removing 5 μmol L-1 of DOC. After 12 days, the surface community began to shift, and DOC quality became less diagenetically altered along with an increase in SAR202, a Chloroflexi that can degrade recalcitrant dissolved organic matter (DOM). Labile DOC production after 12 days coincided with an increase of Nitrosopumilales, a chemoautotrophic ammonia oxidizing archaea (AOA) that converts ammonia to nitrite based on the ammonia monooxygenase (amoA) gene copy number and nutrient data. In comparison, the inoculation of the deep anaerobic prokaryotic community into surface 0.2 μm filtrate demonstrated a die-off of 25.5% of the initial inoculum community followed by a 1.5-fold increase in cell densities over 6 days. Within 2 days, the prokaryotic community shifted from a Chlorobiales dominated assemblage to a surface-like heterotrophic community devoid of Chlorobiales. The DOM quality changed to less diagenetically altered material and coincided with an increase in the ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) gene number followed by an influx of labile DOM. Upon reoxygenation, the deep DOM that accumulated under suboxic conditions is bioavailable to surface prokaryotes that utilize the accumulated DOC initially before switching to a community that can both produce labile DOM via chemoautotrophy and degrade the more recalcitrant DOM.

Land-Water Transport and Sources of Nitrogen Pollution Affecting the Structure and Function of Riverine Microbial Communities.

The characterization of variations in riverine microbiota that stem from contaminant sources and transport modes is important for understanding biogeochemical processes. However, the association between complex anthropogenic nitrogen pollution and bacteria has not been extensively investigated owing to the difficulties faced while determining the distribution of nitrogen contaminants in watersheds. Here, we employed the Soil and Water Assessment Tool alongside microbiological analysis to explore microbial characteristics and their responses to complex nitrogen pollution patterns. Significant variations in microbial communities were observed in sub-basins with distinct land-water pollution transport modes. Point source-dominated areas (PSDAs) exhibited reduced microbial diversity, high number of denitrification groups, and increased nitrogen cycling compared with others. The negative relative deviations (-3.38) between the measured and simulated nitrate concentrations in PSDAs indicated that nitrate removal was more effective in PSDAs. Pollution sources were also closely associated with microbiota. Effluents from concentrated animal feeding operations were the primary factors relating to the microbiota compositions in PSDAs and balanced areas. In nonpoint source-dominated areas, contaminants from septic tanks become the most relevant sources to microbial community structures. Overall, this study expands our knowledge regarding microbial biogeochemistry in catchments and beyond by linking specific nitrogen pollution scenarios to microorganisms.

The microbiome of cryospheric ecosystems

The melting of the cryosphere is among the most conspicuous consequences of climate change, with impacts on microbial life and related biogeochemistry. However, we are missing a systematic understanding of microbiome structure and function across cryospheric ecosystems. Here, we present a global inventory of the microbiome from snow, ice, permafrost soils, and both coastal and freshwater ecosystems under glacier influence. Combining phylogenetic and taxonomic approaches, we find that these cryospheric ecosystems, despite their particularities, share a microbiome with representatives across the bacterial tree of life and apparent signatures of early and constrained radiation. In addition, we use metagenomic analyses to define the genetic repertoire of cryospheric bacteria. Our work provides a reference resource for future studies on climate change microbiology.

Uniting the scales of microbial biogeochemistry with trait‐based modelling

Abstract Below‐ground microbial communities drive some of Earth's largest biogeochemical fluxes, yet they represent a major source of uncertainty in global biogeochemical models. This review synthesizes recent advances in trait‐based soil carbon modelling in order to identify how empirical observations of microbial traits can inform the next generation of soil carbon models. We identify four key perspectives from which trait‐based models have investigated the role of microbes in soil carbon fluxes, ranging from the largest to the smallest scales of biological organization: (i) Earth system models, which have recently begun to incorporate microbial traits at a global scale; (ii) ecosystem models, which relate microbial carbon cycling to other trophic levels and element cycles; (iii) models from community ecology, which link theories of species diversity to ecosystem cycles; and (iv) models of fine‐scale physiology, which mechanistically represent traits at the individual level. Highlighting the contributions of diverse trait‐based modelling approaches, we caution that this diversity makes it challenging to link perspectives at different scales. The meaning of a trait depends both on the structure of the model in which it occurs and on the scale treated by the model. Thus, reapplying a fine‐scale trait at a broader scale may make incorrect predictions, an issue we illustrate quantitatively using model simulations. With these challenges in mind, we highlight several ways to synthesize the scales of microbial biogeochemical modelling: (i) quantitatively, using mathematical scaling techniques, (ii) empirically, by applying experiments to test relationships between scales and (iii) conceptually, by identifying key traits and processes across scales. Taking full advantage of trait‐based modelling, ecologists will thus be able to incorporate multiple perspectives to better predict carbon cycling in a changing world. Read the free Plain Language Summary for this article on the Journal blog.

Microbial community composition, dynamics, and biogeochemistry during the start-up of a partial nitritation-anammox pathway in an upflow reactor

The dynamics of the microbial community and functional taxa related to nitrogen (N) removal biogeochemical processes can be important to the development of new cost-effective processes in wastewater treatment. This work consisted of the start-up of an upflow reactor for N-removal by partial nitritation/anammox pathway, working at ambient temperature, during 397 d. After an adaptation to the reactor operational conditions, a stable total N-removal (52% efficiency) was linked to ammonium deletion. High-throughput sequencing of 16S rRNA gene amplicons analysis revealed a relative abundance of about 1% of anammox genus Candidatus Brocadia after 397 d. Nitrosomonas, a nitrifying bacterium also increased the relative abundance, together with the accretion of relative numbers of Denitratisoma and Thiobacillus, recognized as heterotrophic and chemolithoautotrophic denitrifying bacteria, respectively. These findings provide a better understanding of the N-removal by key microbial groups that may be useful to optimize future field application of systems working at ambient temperature.

Microbial biogeochemistry and phosphorus limitation in cryoconite holes on glaciers across the Taylor Valley, McMurdo Dry Valleys, Antarctica

Microbial biogeochemistry and phosphorus limitation in cryoconite holes on glaciers across the Taylor Valley, McMurdo Dry Valleys, Antarctica

Woolly beech aphid infestation reduces soil organic carbon availability and alters phyllosphere and rhizosphere bacterial microbiomes

PurposeThe woolly beech aphid thrives on European beech leaves, which has complex direct and indirect impacts on above- and belowground processes. A mechanistic understanding of insect-mediated changes in organic carbon (OC) availability for microbial life and its implications for element cycling is still lacking. This study aims at disentangling aphid-induced effects on phyllosphere and rhizosphere bacterial communities, as well as investigating feedbacks to OC transfer from the canopy to the mineral soil.MethodsFollowing 2.5 months of infestation, we tracked the fate of OC (13CO2 pulse-labelling) in several compartments of beech sapling – soil mesocosms over 5 days. In ecosystem solutions, water extracts and soil/plant compartments we determined OC and N and solid δ13C. Bacterial community structure (16S rRNA gene targeted amplicon sequencing and quantitative PCR) and metabolite profiles (LC-qTOF-MS) were analysed.ResultsWe found significantly higher aphid-mediated inputs of OC within throughfall. Honeydew-derived C on infested leaves was inconsequential for total phyllosphere bacterial abundances, but verifiably affected the community structure. In all soil compartments, cold-water extractable OC pools declined significantly by frequent inputs of readily available OC. This pattern might relate to reductions in rhizodepositions and altered microbial processing by accelerated soil C-mineralization. As a result, the abundance of metabolites changed significantly in different ecosystem solutions.ConclusionsOur findings attest that insect infestations induce distinct direct and indirect effects on plant-insect-microbiome interactions leading to marked alterations in C dynamics. This integrated approach improves our understanding on microbial dynamics and biogeochemistry and evaluates the role of insects for ecosystem processes.

Hydrological properties predict the composition of microbial communities cycling methane and nitrogen in rivers

Sediment microbial communities drive the biogeochemical cycles that make rivers globally important sources and sinks of carbon (C) and nitrogen (N). The structure of these communities is strongly determined by the local physico-chemical environment. However, we currently lack an understanding of the factors that determine microbial community structures at the catchment scale. Here, we show that the contribution of groundwater to total river flow (quantified as base flow index; BFI) predicts the structure and diversity of the different microbial functional groups that cycle N and C across nine UK rivers, spanning a geological BFI gradient from 0.23 (clay sediment) to 0.95 (chalk gravel sediment). Furthermore, the GC-content (percentage of guanine-cytosine bases in a DNA sequence) and codon-usage bias of ammonia monooxygenase DNA sequences, and the hydrophobicity and net-charge of the corresponding amino acid sequences, were all strongly correlated with BFI, likely reflecting physiological adaptations to different riverbed sediment structure along the BFI gradient. Our results offer an opportunity to overcome the “paradox of scales” that has seen microbial ecologists focus on small- rather than large-scale environmental variables, enabling us to scale-up our understanding of microbial biogeochemistry to the catchment and beyond.

Shining new light into soil systems: Spectroscopy in microfluidic soil chips reveals microbial biogeochemistry

Microfluidic soil chips render optical access to the naturally opaque soil systems and enable direct investigation of microbial growth and interactions in micro-structurally and chemically controlled environments. However, chemical analyses of these interactions at high spatial and temporal resolution are still lacking. Here we propose that the use of advanced microspectroscopy techniques, namely infrared absorption, Raman scattering and synchrotron radiation based X-ray microspectroscopy, in microfluidic soil chips would make it possible to approach these phenomena. They allow monitoring biogeochemical processes in and around soil microbial cells growing in the reproducibly designed microenvironments within the chips at (sub)micrometer scale. Complementary use of several of the microspectroscopy techniques is beneficial for obtaining information about both molecular and elemental composition, oxidation states and local structure of the elements in the sample. Ultimately, we argue that microspectroscopy in microfluidic chips can lead to relevant breakthroughs in frontier research areas in soil science, such as (1) analysis of chemical responses of microbes to environmental triggers at micro-scale spatial resolution, (2) phenotypical identification and phylogenetic classification of single cells of soil microbes in situ, (3) determining spatially and time resolved effects of heavy metals and organic pollutants, including microplastics, on soils and (4) spatially resolved analysis of soil organic matter dynamics for better understanding of soil carbon storage. Tailoring the chip design to achieve optical transparency to the radiation type used by the different microspectroscopy methods is crucial to achieve this; therefore, we expect that this perspective will inspire the scientific community to use the proposed approaches and thus push both the technical development of the microspectroscopy suitable soil chips and the research frontier in soil science.

An Introduction to “Microbial Biogeochemistry: A Special Issue of Aquatic Geochemistry Honoring Mark Hines”

An Introduction to “Microbial Biogeochemistry: A Special Issue of Aquatic Geochemistry Honoring Mark Hines”

Editorial: Metagenomics in Limnology and Oceanography

The publication of this special issue, “Linking metagenomics to aquatic microbial ecology,” in Limnology and Oceanography, is long overdue. But perhaps it could not have appeared in L&O any earlier. The term “metagenomics” was invented in the late 1990s to describe the retrieval of genetic information from microorganisms without preselection by PCR, which gets only the targeted gene, or by isolating and culturing the organisms in the lab, which gets only a few microbes. Before metagenomics, microbial ecologists were well on their way to identifying microorganisms by using approaches that focused on the genes for ribosomal RNA. But with few exceptions, the rRNA gene data did not say much about what the organisms do—their role in ecological and biogeochemical processes. Metagenomic data tell us about their potential roles, and the other “omic” approaches (metatranscriptomics, metaproteomics, and so on) get closer to their ongoing activity. Metagenomics and its relatives took over microbial ecology after 2000, as documented by Pep Gasol's analysis of publications in the field since 1980 (Microbial Ecology of the Oceans, third edition 2018). Pep found that metagenomics started to have an impact, as measured by citation numbers, at least 10 years ago. Until this special issue, the metagenomic wave has left L&O largely untouched. According to the Web of Science, out of the nearly 10,000 papers published in the journal since its beginning, only seven report metagenomic results. An additional two papers have metatranscriptomic data, while no L&O paper has metaproteomic or other omic data from organisms. By contrast, since its start in 2007, the ISME Journal has published 432 metagenomic papers. All seven of the L&O metagenomic papers appeared after 2009, which so happens is when I published a primer about metagenomics and other omics in the L&O Bulletin at the invitation of then editor, John Dolan. (In case you are wondering, the L&O Bulletin article is why Deputy Editor-in-Chief Maggie Xenopoulos thought of me for this piece.) My article did not exactly launch an avalanche of papers on the topic. While this special issue appears late in metagenomic history, arguably it is appearing in L&O at just about the right time. The field has evolved to the point where it can now more forcefully explore questions of interest to L&O readers, as discussed in the issue's introduction by Grossart et al. Where once even extracting DNA was challenging, metagenomic methods now can be used by many L&O readers, not just the specialists who developed the methods. These methods have also gotten cheaper. In particular, sequencing costs have declined dramatically while sequencing power has exploded beyond belief. Because of the huge decrease in costs, microbial ecologists can analyze more samples and explore ecological and biogeochemical questions that were not feasible until recently. Metagenomic-wielding investigators can now take more time points or sample more locations; replication is no longer a foreign word. In this regard, a metagenomic paper is starting to look more like a typical L&O paper. Finally, after being dominated by work in the oceans for many years, metagenomics is catching up to the range of aquatic habitats covered by L&O. Reflecting the recent growth in freshwater omics, this special issue has more freshwater papers than marine ones (16 vs. 6). I suppose purely oceanographic methods have appeared in L&O, but it seems appropriate that this freshwater-dominated special issue is coming out in a journal published by a society that started in 1936 as the Limnological Society of America. I hope this special issue will encourage more omic papers in L&O. The journal needs these papers if it is to see the latest advances in microbial ecology and microbial biogeochemistry. It would be an exaggeration to say that metagenomics needs L&O. But publication of more omic papers in L&O would signal a maturation of the field, that it is focusing less on methodology and more on understanding microbial communities and processes. Of course, metagenomics has already contributed many new insights into the ecology and biogeochemistry of microbes. This special issue shows how it can do even more.

Microbial Community Structure and Metabolic Potential of the Hyporheic Zone of a Large Mid-Stream Channel Bar

To develop a greater understanding of hyporheic zone microbial biogeochemistry, we sampled pore fluids from a piezometer array associated with the McCarran Ranch channel bar (MRCB); a partially submerged cobble island in the Truckee River, NV, USA. Flowing surface water and pumped pore fluids were characterized by prokaryotic community structure, metabolic potential, and aqueous physicochemistry. Concentrations of potential respiratory electron acceptors were highest in surface water and riverbed porewater and sequentially depleted in porewaters along the inferred flowpath (O2, then NO3−, then SO42−). Correspondingly, cultivable nitrate reducers/denitrifiers were most abundant in surface water and riverbed porewater, despite oxic conditions. Cultivable sulfate reducers were overall most abundant in surface water. Prokaryotic community reconstruction from 16S rRNA gene sequences indicates that the surface water community was less diverse than that of porewater and supports a shift in metabolic strategy, from aerobic heterotrophy in surface water (e.g., Comamonadaceae and Sporichthyaceae) to chemolithotrophy and anaerobic metabolisms (e.g., Hydrogenophaga spp., Ferribacterium spp., Methanobacterium spp.) along the hyporheic flow path. These data indicate that prokaryotic communities within the MRCB are phylogenetically and metabolically diverse and contribute to biogeochemical cycling in this common yet relatively understudied habitat.

Evolving paradigms in biological carbon cycling in the ocean

ABSTRACT Carbon is a keystone element in global biogeochemical cycles. It plays a fundamental role in biotic and abiotic processes in the ocean, which intertwine to mediate the chemistry and redox status of carbon in the ocean and the atmosphere. The interactions between abiotic and biogenic carbon (e.g. CO2, CaCO3, organic matter) in the ocean are complex, and there is a half-century-old enigma about the existence of a huge reservoir of recalcitrant dissolved organic carbon (RDOC) that equates to the magnitude of the pool of atmospheric CO2. The concepts of the biological carbon pump (BCP) and the microbial loop (ML) shaped our understanding of the marine carbon cycle. The more recent concept of the microbial carbon pump (MCP), which is closely connected to those of the BCP and the ML, explicitly considers the significance of the ocean's RDOC reservoir and provides a mechanistic framework for the exploration of its formation and persistence. Understanding of the MCP has benefited from advanced ‘omics’ and novel research in biological oceanography and microbial biogeochemistry. The need to predict the ocean's response to climate change makes an integrative understanding of the BCP, ML and MCP a high priority. In this review, we summarize and discuss progress since the proposal of the MCP in 2010 and formulate research questions for the future.

Mercury methylation in stormwater retention ponds at different stages in the management lifecycle.

Stormwater retention ponds effectively manage erosion, flooding, and pollutant loadings, but are also sources of methylmercury (MeHg), a bioaccumulative neurotoxin which is produced by anaerobic aquatic microorganisms. Stormwater retention ponds have a 10-15 year working life, after which they are dredged and reflooded. In this study, we related MeHg biogeochemistry to the different stages of the management lifecycle. In a new, a dredged, and a mature stormwater retention pond, we measured MeHg and inorganic mercury (IHg) concentrations, and the potential for MeHg formation (Kmeth), during the early summer, peak summer, and fall of 2013. In our study sites, MeHg concentrations appear to be driven by mercury (Hg) methylation, indicated by significant correlations between Kmeth values and MeHg concentrations and the percent of Hg present as MeHg. Relationships between Hg variables and ancillary biogeochemistry suggest that Hg methylation is carried out by sulfate reducing bacteria, but that the process is modulated by the supply of IHg substrate, sediment total and labile organic carbon, and possibly competition with nitrate reducers. Wetlands at different points in the management lifecycle differ in terms of their MeHg biogeochemistry. The organic matter-poor new wetland had low MeHg production (mean Kmeth 0.014 per day) and sediment concentrations (mean 0.015 ng g-1), while the mature wetland both produced and accumulated MeHg about five times more actively. Methylmercury production capacity was only temporarily reduced in the reflooded sediments of the dredged wetland, which experienced rapid increases in Kmeth values from low (mean 0.015 per day) immediately after dredging, to values similar to those in the mature wetland after five months. This pattern may have been related to recolonization of the sediments with mercury methylators or increased microbial activities in response to the addition of fresh organic matter. Additional studies should focus on the applicability of these patterns to stormwater retention ponds in other areas, and particularly investigate the effects of stormwater pond dredging on their microbial ecology and MeHg biogeochemistry.

Novel Microbial Assemblages Dominate Weathered Sulfide-Bearing Rock from Copper-Nickel Deposits in the Duluth Complex, Minnesota, USA.

The Duluth Complex in northeastern Minnesota hosts economically significant deposits of copper, nickel, and platinum group elements (PGEs). The primary sulfide mineralogy of these deposits includes the minerals pyrrhotite, chalcopyrite, pentlandite, and cubanite, and weathering experiments show that most sulfide-bearing rock from the Duluth Complex generates moderately acidic leachate (pH 4 to 6). Microorganisms are important catalysts for metal sulfide oxidation and could influence the quality of water from mines in the Duluth Complex. Nevertheless, compared with that of extremely acidic environments, much less is known about the microbial ecology of moderately acidic sulfide-bearing mine waste, and so existing information may have little relevance to those microorganisms catalyzing oxidation reactions in the Duluth Complex. Here, we characterized the microbial communities in decade-long weathering experiments (kinetic tests) conducted on crushed rock and tailings from the Duluth Complex. Analyses of 16S rRNA genes and transcripts showed that differences among microbial communities correspond to pH, rock type, and experimental treatment. Moreover, microbial communities from the weathered Duluth Complex rock were dominated by taxa that are not typically associated with acidic mine waste. The most abundant operational taxonomic units (OTUs) were from the genera Meiothermus and Sulfuriferula, as well as from diverse clades of uncultivated Chloroflexi, Acidobacteria, and Betaproteobacteria Specific taxa, including putative sulfur-oxidizing Sulfuriferula spp., appeared to be primarily associated with Duluth Complex rock, but not pyrite-bearing rocks subjected to the same experimental treatment. We discuss the implications of these results for the microbial ecology of moderately acidic mine waste with low sulfide content, as well as for kinetic testing of mine waste.IMPORTANCE Economic sulfide mineral deposits in the Duluth Complex may represent the largest undeveloped source of copper and nickel on Earth. Microorganisms are important catalysts for sulfide mineral oxidation, and research on extreme acidophiles has improved our ability to manage and remediate mine wastes. We found that the microbial assemblages associated with weathered rock from the Duluth Complex are dominated by organisms not widely associated with mine waste or mining-impacted environments, and we describe geochemical and experimental influences on community composition. This report will be a useful foundation for understanding the microbial biogeochemistry of moderately acidic mine waste from these and similar deposits.

Needles in the blue sea: sub-species specificity in targeted protein biomarker analyses within the vast oceanic microbial metaproteome.

Proteomics has great potential for studies of marine microbial biogeochemistry, yet high microbial diversity in many locales presents us with unique challenges. We addressed this challenge with a targeted metaproteomics workflow for NtcA and P-II, two nitrogen regulatory proteins, and demonstrated its application for cyanobacterial taxa within microbial samples from the Central Pacific Ocean. Using METATRYP, an open-source Python toolkit, we examined the number of shared (redundant) tryptic peptides in representative marine microbes, with the number of tryptic peptides shared between different species typically being 1% or less. The related cyanobacteria Prochlorococcus and Synechococcus shared an average of 4.8 ± 1.9% of their tryptic peptides, while shared intraspecies peptides were higher, 13 ± 15% shared peptides between 12 Prochlorococcus genomes. An NtcA peptide was found to target multiple cyanobacteria species, whereas a P-II peptide showed specificity to the high-light Prochlorococcus ecotype. Distributions of NtcA and P-II in the Central Pacific Ocean were similar except at the Equator likely due to differential nitrogen stress responses between Prochlorococcus and Synechococcus. The number of unique tryptic peptides coded for within three combined oceanic microbial metagenomes was estimated to be ∼4 × 10(7) , 1000-fold larger than an individual microbial proteome and 27-fold larger than the human proteome, yet still 20 orders of magnitude lower than the peptide diversity possible in all protein space, implying that peptide mapping algorithms should be able to withstand the added level of complexity in metaproteomic samples.

Dominance of sulfur-fueled iron oxide reduction in low-sulfate freshwater sediments

A central tenant in microbial biogeochemistry is that microbial metabolisms follow a predictable sequence of terminal electron acceptors based on the energetic yield for the reaction. It is thereby oftentimes assumed that microbial respiration of ferric iron outcompetes sulfate in all but high-sulfate systems, and thus sulfide has little influence on freshwater or terrestrial iron cycling. Observations of sulfate reduction in low-sulfate environments have been attributed to the presumed presence of highly crystalline iron oxides allowing sulfate reduction to be more energetically favored. Here we identified the iron-reducing processes under low-sulfate conditions within columns containing freshwater sediments amended with structurally diverse iron oxides and fermentation products that fuel anaerobic respiration. We show that despite low sulfate concentrations and regardless of iron oxide substrate (ferrihydrite, Al-ferrihydrite, goethite, hematite), sulfidization was a dominant pathway in iron reduction. This process was mediated by (re)cycling of sulfur upon reaction of sulfide and iron oxides to support continued sulfur-based respiration--a cryptic sulfur cycle involving generation and consumption of sulfur intermediates. Although canonical iron respiration was not observed in the sediments amended with the more crystalline iron oxides, iron respiration did become dominant in the presence of ferrihydrite once sulfate was consumed. Thus, despite more favorable energetics, ferrihydrite reduction did not precede sulfate reduction and instead an inverse redox zonation was observed. These findings indicate that sulfur (re)cycling is a dominant force in iron cycling even in low-sulfate systems and in a manner difficult to predict using the classical thermodynamic ladder.