A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide.

Subsurface environments are among Earth's largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments.

Long-term climate and hydrologic regimes shape stream invertebrate community responses to a hurricane disturbance.

Disturbances can produce a spectrum of short- and long-term ecological consequences that depend on complex interactions of the characteristics of the event, antecedent environmental conditions, and the intrinsic properties of resistance and resilience of the affected biological system. We used Hurricane Harvey's impact on coastal rivers of Texas to examine the roles of storm-related changes in hydrology and long-term precipitation regime on the response of stream invertebrate communities to hurricane disturbance. We detected declines in richness, diversity and total abundance following the storm, but responses were strongly tied to direct and indirect effects of long-term aridity and short-term changes in stream hydrology.

Genome characterization of two novel deep-sea sediment fungi, Penicillium pacificagyrus sp. nov. and Penicillium pacificasedimenti sp. nov., from South Pacific Gyre subseafloor sediments, highlights survivability.

Background: Marine deep subsurface sediments were once thought to be devoid of eukaryotic life, but advances in molecular technology have unlocked the presence and activity of well-known closely related terrestrial and marine fungi. Commonly detected fungi in deep marine sediment environments includes Penicillium, Aspergillus, Cladosporium, Fusarium, and Schizophyllum, which could have important implications in carbon and nitrogen cycling in this isolated environment. In order to determine the diversity and unknown metabolic capabilities of fungi in deep-sea sediments, their genomes need to be fully analyzed.

Microbial survival mechanisms within serpentinizing Mariana forearc sediments.

Marine deep subsurface sediment is often a microbial environment under energy-limited conditions. However, microbial life has been found to persist and even thrive in deep subsurface environments. The Mariana forearc represents an ideal location for determining how microbial life can withstand extreme conditions including pH 10-12.

Draft Genome Sequences of sp. Strains Isolated from Stranded Septic Bottlenose Dolphins in Alabama, USA.

We report the genome sequences of two isolates from fatal cases of sepsis in bottlenose dolphins (Tursiops truncatus). The genomes were found to be most closely related to Erysipelothrix rhusiopathiae and Erysipelothrix piscisicarius. This information expands our knowledge of the genetic characteristics of this pathogen, which can affect free-ranging marine mammals.

A general pattern of trade-offs between ecosystem resistance and resilience to tropical cyclones.

Tropical cyclones drive coastal ecosystem dynamics, and their frequency, intensity, and spatial distribution are predicted to shift with climate change. Patterns of resistance and resilience were synthesized for 4138 ecosystem time series from = 26 storms occurring between 1985 and 2018 in the Northern Hemisphere to predict how coastal ecosystems will respond to future disturbance regimes. Data were grouped by ecosystems (fresh water, salt water, terrestrial, and wetland) and response categories (biogeochemistry, hydrography, mobile biota, sedentary fauna, and vascular plants).

Redefining the Subsurface Biosphere: Characterization of Fungi Isolated From Energy-Limited Marine Deep Subsurface Sediment.

The characterization of metabolically active fungal isolates within the deep marine subsurface will alter current ecosystem models and living biomass estimates that are limited to bacterial and archaeal populations. Although marine fungi have been studied for over fifty years, a detailed description of fungal populations within the deep subsurface is lacking. Fungi possess metabolic pathways capable of utilizing previously considered non-bioavailable energy reserves.

Draft Genome Sequences of Idiomarina abyssalis Strain KJE, Marinobacter salarius Strain NP2017, and Marinobacter salarius Strain AT3901, Isolated from Deep-Sea Sediment near the Western Flank of the Mid-Atlantic Ridge.

We report the draft genomes of environmental cultures collected from shallow sediment from the western flank of the Mid-Atlantic Ridge. The isolates were most closely related to strain KJE (100% complete), strain NP2017 (97.6% complete), and strain AT3901 (98.

Diversity, Ecology, and Prevalence of Antimicrobials in Nature.

Microorganisms possess a variety of survival mechanisms, including the production of antimicrobials that function to kill and/or inhibit the growth of competing microorganisms. Studies of antimicrobial production have largely been driven by the medical community in response to the rise in antibiotic-resistant microorganisms and have involved isolated pure cultures under artificial laboratory conditions neglecting the important ecological roles of these compounds. The search for new natural products has extended to biofilms, soil, oceans, coral reefs, and shallow coastal sediments; however, the marine deep subsurface biosphere may be an untapped repository for novel antimicrobial discovery.

The Majority of Active in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions.

General studies on benthic microbial communities focus on fundamental biogeochemical processes or the most abundant constituents. Thereby, minor fractions such as the are frequently neglected. Even though this family belongs to the most widely distributed bacteria in the marine environment, their proportion on benthic microbial communities is usually within or below the single digit range.

Draft Genome Sequences of spp. from Deeply Buried Oligotrophic Marine Sediments.

Here, we report genome sequences of two isolates from below the seafloor of the oligotrophic South Pacific Gyre. These genomes are the first reported for fungi from deeply buried marine sediment. Both genomes will provide valuable information regarding the role of fungi and carbon cycling in the energy-limited subsurface biosphere.

Sediment Microbial Communities Influenced by Cool Hydrothermal Fluid Migration.

Cool hydrothermal systems (CHSs) are prevalent across the seafloor and discharge fluid volumes that rival oceanic input from rivers, yet the microbial ecology of these systems are poorly constrained. The Dorado Outcrop on the ridge flank of the Cocos Plate in the northeastern tropical Pacific Ocean is the first confirmed CHS, discharging minimally altered <15°C fluid from the shallow lithosphere through diffuse venting and seepage. In this paper, we characterize the resident sediment microbial communities influenced by cool hydrothermal advection, which is evident from nitrate and oxygen concentrations.

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life.

Earth's subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high.

Major phylum-level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface.

Earth's deep subsurface biosphere (DSB) is home to a vast number and wide variety of microorganisms. Although difficult to access and sample, deep subsurface environments have been probed through drilling programs, exploration of mines and sampling of deeply sourced vents and springs. In an effort to understand the ecology of deep terrestrial habitats, we examined bacterial diversity in the Sanford Underground Research Facility (SURF), the former Homestake gold mine, in South Dakota, USA.

A novel cohabitation between two diazotrophic cyanobacteria in the oligotrophic ocean.

The cyanobacterial genus Trichodesmium is biogeochemically significant because of its dual role in nitrogen and carbon fixation in the oligotrophic ocean. Trichodesmium species form colonies that can be easily enriched from the water column and used for shipboard rate measurements to estimate their contribution to oceanic carbon and nitrogen budgets. During a July 2010 cruise near the Hawaiian Islands in the oligotrophic North Pacific Subtropical Gyre, a specific morphology of Trichodesmium puff-form colonies were examined under epifluorescent microscopy and found to harbor a colonial endobiont, morphologically identified as the heterocystous diazotrophic cyanobacterium Calothrix.

Microbial activity in the marine deep biosphere: progress and prospects.

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists-all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes.

Characterization of Metabolically Active Bacterial Populations in Subseafloor Nankai Trough Sediments above, within, and below the Sulfate-Methane Transition Zone.

A remarkable number of microbial cells have been enumerated within subseafloor sediments, suggesting a biological impact on geochemical processes in the subseafloor habitat. However, the metabolically active fraction of these populations is largely uncharacterized. In this study, an RNA-based molecular approach was used to determine the diversity and community structure of metabolically active bacterial populations in the upper sedimentary formation of the Nankai Trough seismogenic zone.

Characterization of Microbial Population Shifts during Sample Storage.

The objective of this study was to determine shifts in the microbial community structure and potential function based on standard Integrated Ocean Drilling Program (IODP) storage procedures for sediment cores. Standard long-term storage protocols maintain sediment temperature at 4°C for mineralogy, geochemical, and/or geotechnical analysis whereas standard microbiological sampling immediately preserves sediments at -80°C. Storage at 4°C does not take into account populations may remain active over geologic time scales at temperatures similar to storage conditions.

Hydrogen sulfide production and volatilization in a polymictic eutrophic saline lake, Salton Sea, California.

The Salton Sea is a large shallow saline lake located in southern California that is noted for high sulfate concentrations, substantial algal productivity, and very warm water column temperatures. These conditions are well-suited for sulfide production, and sulfide has been implicated in summer fish kills, although no studies have been conducted to specifically understand hydrogen sulfide production and volatilization there. Despite polymictic mixing patterns and relatively short accumulation periods, the amount of sulfide produced is comparable to meromictic lakes.

Perchlorate in groundwater: a synoptic survey of "pristine" sites in the coterminous United States.

Perchlorate is widely used as an oxidant in solid rocket propellants and energetic applications, and it has frequently been detected in groundwaters at concentrations relevant to human health. The possibility of naturally occurring perchlorate has only recently received significant attention. Relying primarily on domestic, agricultural, and recreational wells, we utilized a network of volunteers to help collect 326 groundwater samples from across the coterminous United States.