Microbial Diversity and Function in Shallow Subsurface Sediment and Oceanic Lithosphere of the Atlantis Massif.

The marine lithospheric subsurface is one of the largest biospheres on Earth; however, little is known about the identity and ecological function of microorganisms found in low abundance in this habitat, though these organisms impact global-scale biogeochemical cycling. Here, we describe the diversity and metabolic potential of sediment and endolithic (within rock) microbial communities found in ultrasmall amounts (101 to 104 cells cm-3) in the subsurface of the Atlantis Massif, an oceanic core complex on the Mid-Atlantic Ridge that was sampled on International Ocean Discovery Program (IODP) Expedition 357. This study used fluorescence-activated cell sorting (FACS) to enable the first amplicon, metagenomic, and single-cell genomic study of the shallow (<20 m below seafloor) subsurface of an actively serpentinizing marine system. The shallow subsurface biosphere of the Atlantis Massif was found to be distinct from communities observed in the nearby Lost City alkaline hydrothermal fluids and chimneys, yet similar to other low-temperature, aerobic subsurface settings. Genes associated with autotrophy were rare, although heterotrophy and aerobic carbon monoxide and formate cycling metabolisms were identified. Overall, this study reveals that the shallow subsurface of an oceanic core complex hosts a biosphere that is not fueled by active serpentinization reactions and by-products. IMPORTANCE The subsurface rock beneath the ocean is one of the largest biospheres on Earth, and microorganisms within influence global-scale nutrient cycles. This biosphere is difficult to study, in part due to the low concentrations of microorganisms that inhabit the vast volume of the marine lithosphere. In spite of the global significance of this biosphere, little is currently known about the microbial ecology of such rock-associated microorganisms. This study describes the identity and genomic potential of microorganisms in the subsurface rock and sediment at the Atlantis Massif, an underwater mountain near the Mid-Atlantic Ridge. To enable our analyses, fluorescence-activated cell sorting (FACS) was used as a means to concentrate cells from low biomass environmental samples for genomic analyses. We found distinct rock-associated microorganisms and found that the capacity for microorganisms to utilize organic carbon was the most prevalent form of carbon cycling. We additionally identified a potential role for carbon monoxide metabolism in the subsurface.

Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems.

Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8 Tara Ocean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15% of aplastidic cell sorts, and 7% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14°N to 20°S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filtered.

129I in Swedish rivers: distribution and sources.

We analyzed the concentration of 129I in the water of 26 rivers covering most of the runoff from Sweden, with the aim of assessing current contamination levels, distribution patterns and potential sources in freshwater systems of northern Europe. The results show relatively high values (up to 1.4 x 10(9) atoms l(-1)), steeply decreasing levels with increasing latitude and a positive correlation with Cl concentration and other chemical parameters. The 129I concentrations observed in south Sweden are probably the highest ever recorded in rivers without any direct discharge from a nuclear installation. The strong latitudinal dependence suggests a northward dilution and possibly depletion of the isotope and a transport from a source located to the south. The most plausible source of the 129I in the studied rivers is atmospheric fallout of 129I emitted either by atmospheric discharges from the nuclear reprocessing facilities at Sellafield (England) and La Hague (France) or by volatilization from seawater contaminated by the same sources. The question is now whether and at what rate the 129I concentration in Nordic watersheds will increase further if discharges from nuclear reprocessing continue.

Differential Dissolved Organic Nitrogen Availability and Bacterial Aminopeptidase Activity in Limnic and Marine Waters.

Abstract Nitrogen often limits primary production in marine ecosystems and its loading from terrestrial sources is the major cause of enhanced coastal eutrophication worldwide. About 70% of nitrogen transported by rivers globally is dissolved organic nitrogen (DON). Therefore, terrestrial DON is potentially an important component of the N dynamics in aquatic ecosystems, but the bioavailability of this organic nitrogen is poorly known. Bacterial extracellular hydrolysis of polymers is a bottleneck in the utilization of natural dissolved organic matter, mostly consisting of high molecular weight compounds. To study the bacterial utilization and extracellular enzymatic hydrolysis of DON, we developed a bioassay employing natural DON as the only N source, and N as the limiting nutrient. Bacterial cell density and activity of an unspecific aminopeptidase (AMPase) were followed in the cultures. Natural DON stimulated the cell-specific AMPase activity. Furthermore, refractory and humus-rich DOM caused a stronger stimulation than labile DOM. We propose that the previously reported inhibitory effect of humic substances on enzyme activity was outweighed by the induction of enzyme synthesis caused by refractory substrates. AMPase activity and the estimated DON bioavailability were more than twofold higher in seawater than in freshwater with identical substrate additions. This indicates that hydrolysis and turnover of land-derived DON is enhanced when it enters coastal marine waters, enabling it to support elevated bacterioplankton and phytoplankton growth.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p264.html

Vertical Patterns of Nitrogen Transformations during Infiltration in Two Wetland Soils.

The (sup15)N isotope dilution and pairing methods were applied to investigate the vertical distribution of nitrogen transformations during infiltration in one peaty soil and one sandy soil. Water containing (sup15)N-nitrate (99.9%; 200 (mu)M) as the only nitrogen fraction was infiltrated through cores containing homogenized soil, with lengths varying from 5.5 to 38 cm. Oxygen and nitrogen dynamics were investigated by measuring inflowing and outflowing water. The experimental design allowed determinations of vertical profiles of aerobic respiration, nitrification, and coupled and uncoupled denitrification and ammonification. In the sandy soil, all oxygen was consumed in the upper 14 cm and nitrate was subsequently consumed and removed, up to a maximum of 70% in the longest core (28 cm). In the peaty soil, oxygen was consumed in the upper 7.5 cm and all nitrate was denitrified in the top 20 cm. In both soils, nitrogen removal by denitrification was counteracted by the release of ammonium and dissolved organic nitrogen. In the sandy soil, net nitrogen removal occurred in cores of 14 cm and longer; in the longest core, 40% was removed. In the peaty soil, release was equal to removal in the top 14 cm but release exceeded removal in the deeper layers, leading to a 100% increase of total nitrogen in the effluent water from the longest core (38 cm).

Nitrogen Transformations in Wetland Soil Cores Measured by (sup15)N Isotope Pairing and Dilution at Four Infiltration Rates.

The effect of water infiltration rate (IR) on nitrogen cycling in a saturated wetland soil was investigated by applying a (sup15)N isotope dilution and pairing method. Water containing [(sup15)N]nitrate was infiltrated through 10-cm-long cores of sieved and homogenized soil at rates of 72, 168, 267, and 638 mm day(sup-1). Then the frequencies of (sup30)N(inf2), (sup29)N(inf2), (sup15)NO(inf3)(sup-), and (sup15)NH(inf4)(sup+) in the outflow water were measured. This method allowed simultaneous determination of nitrification, coupled and uncoupled denitrification, and nitrate assimilation rates. From 3% (at the highest IR) to 95% (at the lowest IR) of nitrate was removed from the water, mainly by denitrification. The nitrate removal was compensated for by the net release of ammonium and dissolved organic nitrogen. Lower oxygen concentrations in the soil at lower IRs led to a sharper decrease in the nitrification rate than in the ammonification rate, and, consequently, more ammonium leaked from the soil. The decreasing organic-carbon-to-nitrogen ratio (from 12.8 to 5.1) and the increasing light A(inf250)/A(inf365) ratio (from 4.5 to 5.2) indicated an increasing bioavailability of the outflowing dissolved organic matter with increasing IR. The efflux of nitrous oxide was also very sensitive to IR and increased severalfold when a zone of low oxygen concentration was close to the outlet of the soil cores. N(inf2)O then constituted 8% of the total gaseous N lost from the soil.