Insights into the origin of N2O in Lake Vida brine

Lake Vida is a briny, frigid, inhospitable anoxic lake, and sealed beneath 16m of ice, there is an 18 to 21% NaCl based brine with a high concentration of N2O. Biological and abiotic denitrification pathways of N2O production were evaluated to determine the origin(s) of the high concentration of N2O in Lake Vida brine. Sixteen bacterial isolates from Lake Vida brine spanning six genera (Marinobacter, Psychrobacter, Exiguobacterium, Arthrobacter, Microbacterium, and Kocuria) were tested for the capability of incomplete or complete denitrification. Four of the sixteen isolates evaluated showed evidence of N2 production. The isolate from each genus that produced the most N2O was further tested to see if total protein production correlated with N2O production. Marinobacter sp. strain LV411 had the highest N2O production rate of 60 ± 6µM day−1 and a generation time of 30 ± 0 hours grown at 10°C. Isolate LV411 produced nearly 8-fold more N2O, than the next highest N2O producer (Exiguobacterium sp. strain LV05br1). Lake Vida bacterial isolates demonstrated the ability to denitrify, in which four of them showed the potential for complete denitrification. The potential, therefore exists that these isolates, Marinobacter sp., in particular, could influence the Lake Vida brine nitrogen biogeochemistry. The total N2O produced by Marinobacter sp. strain LV411 and Psychrobacter sp. strain LV181 each had a SP value around 0 / that is similar to that reported previously for production by denitrifying bacteria. The net isotope effect values for δ15N, δ18O, and SP for LV411 and LV181 were different from each other, suggesting different fractionation factors along the denitrification pathway. The potential for abiotic denitrification in Lake Vida brine was also demonstrated. The addition of ferrous iron (Fe2+), nitrite (NO2−), or nitrate (NO3−) stimulated N2O production in mercuric chloride (HgCl2) amended Lake Vida brine. A 15N tracer experiment, using Lake Vida brine, revealed a decrease in N2O concentration in several amendments with a decrease in δ15N bulk isotope values, confirming N2O production and suggesting further reduction of N2O to N2. Lake Vida brine treated with 10mM FeSO4 and 10mM NaNO2 had a N2O production rate of 10µM day−1, a final SP value of −1.5 ± 0.5 /, a final δ15N value of 24.9 ± 0.4 /, and a final δ18O value of −14.5 ± 0.1 /. The SP value is within the range of SP values reported from chemodenitrification. The addition of Fe2+, NO2−, or NO3− also stimulated CO2 production in HgCl2 amended Lake Vida brine, likely from acidification of the large reservoir of DIC in Lake Vida brine. The N2O SP values from biological and abiotic sources in Lake Vida were not significantly different and therefore cannot be used to discern a difference between the two sources (Marinobacter sp. strain LV411 was 1.2 ± 0.7 /, Psychrobacter sp. strain LV181 was −1.9 ± 0.8 / and abiotic treatment with 10mM FeSO4 + 10mM NaNO2 was −1.5 ± 0.5 /). A comparison of N2O SP values, along with evidence of possible biological and abiotic N2O production, suggests the source of N2O in Lake Vida brine could be the result of either process or a combination of both biological and abiotic sources

Coming-of-age characterization of soil viruses: A user’s guide to virus isolation, detection within metagenomes, and viromics

The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology

Coming-of-age characterization of soil viruses: A user’s guide to virus isolation, detection within metagenomes, and viromics

The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology

Permafrost as a potential pathogen reservoir

The Arctic is currently warming at unprecedented rates because of global climate change, resulting in thawing of large tracts of permafrost soil. A great challenge is understanding the implications of permafrost thaw on human health and the environment. Permafrost is a reservoir of mostly uncharacterized microorganisms and viruses, many of which could be viable. Given our limited knowledge of permafrost-resident microbes, we also lack the basis to judge whether they pose risks to humans, animals, and plants. Here we delve into features of permafrost as a microbial habitat and discuss what is known about the potential for microbial pathogens to emerge in a warming climate as permafrost thaws. This review has broader implications for human health and ecosystem sustainability in the new Arctic environment that will emerge from a thawed permafrost landscape

The IsoGenie database : an interdisciplinary data management solution for ecosystems biology and environmental research

Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project’s interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team’s modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB’s expandability and flexible architecture allow it to serve as an example ecosystems database

The IsoGenie database: An interdisciplinary data management solution for ecosystems biology and environmental research

Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.Ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project's interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team's modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB's expandability and flexible architecture allow it to serve as an example ecosystems database