Jody W. Deming

Bacterial Activity at −2 to −20°C in Arctic Wintertime Sea Ice

ABSTRACT Arctic wintertime sea-ice cores, characterized by a temperature gradient of −2 to −20°C, were investigated to better understand constraints on bacterial abundance, activity, and diversity at subzero temperatures. With the fluorescent stains 4′,6′-diamidino-2-phenylindole 2HCl (DAPI) (for DNA) and 5-cyano-2,3-ditoyl tetrazolium chloride (CTC) (for O2-based respiration), the abundances of total, particle-associated (>3-μm), free-living, and actively respiring bacteria were determined for ice-core samples melted at their in situ temperatures (−2 to −20°C) and at the corresponding salinities of their brine inclusions (38 to 209 ppt). Fluorescence in situ hybridization was applied to determine the proportions of Bacteria, Cytophaga-Flavobacteria-Bacteroides (CFB), and Archaea. Microtome-prepared ice sections also were examined microscopically under in situ conditions to evaluate bacterial abundance (by DAPI staining) and particle associations within the brine-inclusion network of the ice. For both melted and intact ice sections, more than 50% of cells were found to be associated with particles or surfaces (sediment grains, detritus, and ice-crystal boundaries). CTC-active bacteria (0.5 to 4% of the total) and cells detectable by rRNA probes (18 to 86% of the total) were found in all ice samples, including the coldest (−20°C), where virtually all active cells were particle associated. The percentage of active bacteria associated with particles increased with decreasing temperature, as did the percentages of CFB (16 to 82% of Bacteria) and Archaea (0.0 to 3.4% of total cells). These results, combined with correlation analyses between bacterial variables and measures of particulate matter in the ice as well as the increase in CFB at lower temperatures, confirm the importance of particle or surface association to bacterial activity at subzero temperatures. Measuring activity down to −20°C adds to the concept that liquid inclusions in frozen environments provide an adequate habitat for active microbial populations on Earth and possibly elsewhere.

Psychrophiles and polar regions

Most reviews of microbial life in cold environments begin with a lament of how little is known about the psychrophilic (cold-loving) inhabitants or their specific adaptations to the cold. This situation is changing, as research becomes better focused by new molecular genetic (and other) approaches, by awareness of accelerated environmental change in polar regions, and by strong interest in the habitability of frozen environments elsewhere in the solar system. This review highlights recent discoveries in molecular adaptation, biodiversity and microbial dynamics in the cold, along with the concept of eutectophiles, organisms living at the critical interface inherent to the phase change of water to ice.

Global Patterns and Predictions of Seafloor Biomass Using Random Forests

A comprehensive seafloor biomass and abundance database has been constructed from 24 oceanographic institutions worldwide within the Census of Marine Life (CoML) field projects. The machine-learning algorithm, Random Forests, was employed to model and predict seafloor standing stocks from surface primary production, water-column integrated and export particulate organic matter (POM), seafloor relief, and bottom water properties. The predictive models explain 63% to 88% of stock variance among the major size groups. Individual and composite maps of predicted global seafloor biomass and abundance are generated for bacteria, meiofauna, macrofauna, and megafauna (invertebrates and fishes). Patterns of benthic standing stocks were positive functions of surface primary production and delivery of the particulate organic carbon (POC) flux to the seafloor. At a regional scale, the census maps illustrate that integrated biomass is highest at the poles, on continental margins associated with coastal upwelling and with broad zones associated with equatorial divergence. Lowest values are consistently encountered on the central abyssal plains of major ocean basins The shift of biomass dominance groups with depth is shown to be affected by the decrease in average body size rather than abundance, presumably due to decrease in quantity and quality of food supply. This biomass census and associated maps are vital components of mechanistic deep-sea food web models and global carbon cycling, and as such provide fundamental information that can be incorporated into evidence-based management.

Deep-sea deposit-feeding strategies suggested by environmental and feeding constraints

The principle of lost opportunity from optimal foraging theory, coupled with recent information about fluxes in the deep sea, allows prediction of feeding behaviours potentially specific to deep-sea deposit feeders. One possible strategy, thus far documented only indirectly, is to ‘ squirrel ’ away rich food from the seasonal or episodic pulses that recently have been shown to fuel meiofaunal growth. Echiurans and sipunculids show morphological and faecal handling patterns consonant with this suggestion. Where it is prevalent, this foraging strategy can have profound effects on stratigraphy. Autocoprophagy is another expected behaviour across a wider taxonomic spectrum, but one that is especially difficult to document. The principle of lost opportunity also predicts highly selective ingestion, not necessarily accomplished by the assessment of individual particles but possibly through pit building in areas where fluids move near-bed material. Under many depositions regimes, small but abundant feeding depressions may be the primary sites where deposition occurs. Conversely, digestive utilization of heterogeneous refractory substrates like humic acids seems as unlikely as an effective municipal waste recycling system that starts with mixed garbage. High gut: body volume ratios in deep-sea deposit feeders, rather than representing an adaptation to use this heterogeneous and refractory end of the food spectrum, instead may allow (through greater residence time of ingested material) greater conversion and absorption of the labile fraction of sediments as it becomes scarcer. Intense natural selection for particle selection ability in fact is one possible reason for the prevalence of meiofauna in the deep sea, and for the diminutive size of macrofaunal taxa there. This selective pressure probably imposes a very restrictive bottleneck on the initial developmental stages of deposit feeders.

The Early Diagenesis of Organic Matter: Bacterial Activity

Bacteria are the primary agents of the early diagenesis of organic matter (OM) in marine sediments. The reasons for their predominant roles are straightforward: (1) they occur abundantly and universally throughout all marine sediments; (2) they can respire, reproduce, and, therefore, use OM more rapidly than any other organisms; (3) they possess enzymes and enzyme systems (in many cases, unique to the prokaryotic kingdom) that make them extraordinarily versatile in their nutritional requirements and abilities to alter a wide variety of particulate and dissolved organic (and inorganic) materials; and (4) they readily enter into complex associations with each other and with higher organisms in ways that produce powerful degradative capabilities beyond those of a single organism in isolation.

A Predictive Model of Bacterial Foraging by Means of Freely Released Extracellular Enzymes

A bstractExtracellular enzymes are important agents for microbial foraging and material cycling in diverse natural and man-made systems. Their abundance and effects are analyzed empirically on scales much larger than the forager. Here, we use a modelling approach to analyze the potential costs and benefits, to an individual immobile microbe, of freely releasing extracellular enzymes into a fluid-bathed, stable matrix of both inert and food-containing particles. The target environments are marine aggregates and sediments, but the results extend to biofilms, bioreactors, soils, stored foods, teeth, gut contents, and even soft tissues attacked by disease organisms. Model predictions, consistent with macroscopic observations of enzyme activity in laboratory and environmental samples, include: support of significant bacterial growth by cell-free enzymes; preponderance of particle-attached, as opposed to dissolved, cell-free enzymes; solubilization of particulate substrates in excess of resident microbe growth requirements; and constitutive, abundant enzyme release in some environments. Feeding with cell-free enzymes appears to be limited to substrates within a well-defined distance of the enzyme source. Fluxes of dissolved organic material out of pelagic oceanic aggregates and marine sediments, and difficulty detecting dissolved enzymes in such environments, may reflect characteristics of cell-free enzyme foraging and properties of the enzymes. Our calculations further suggest that cell-free enzymes may often be used by microorganisms as the fastest means to search for food.

Exopolymer alteration of physical properties of sea ice and implications for ice habitability and biogeochemistry in a warmer Arctic

The physical properties of Arctic sea ice determine its habitability. Whether ice-dwelling organisms can change those properties has rarely been addressed. Following discovery that sea ice contains an abundance of gelatinous extracellular polymeric substances (EPS), we examined the effects of algal EPS on the microstructure and salt retention of ice grown from saline solutions containing EPS from a culture of the sea-ice diatom, Melosira arctica. We also experimented with xanthan gum and with EPS from a culture of the cold-adapted bacterium Colwellia psychrerythraea strain 34H. Quantitative microscopic analyses of the artificial ice containing Melosira EPS revealed convoluted ice-pore morphologies of high fractal dimension, mimicking features found in EPS-rich coastal sea ice, whereas EPS-free (control) ice featured much simpler pore geometries. A heat-sensitive glycoprotein fraction of Melosira EPS accounted for complex pore morphologies. Although all tested forms of EPS increased bulk ice salinity (by 11–59%) above the controls, ice containing native Melosira EPS retained the most salt. EPS effects on ice and pore microstructure improve sea ice habitability, survivability, and potential for increased primary productivity, even as they may alter the persistence and biogeochemical imprint of sea ice on the surface ocean in a warming climate.

Isolation of an Obligately Barophilic Bacterium and Description of a New Genus, Colwellia gen. nov.

Summary An obligately barophilic bacterium, designated strain BNL-1, was isolated in the laboratory, under deepsea conditions of 2 °C and 740 atm hydrostatic pressure, from a sample of particle-rich seawater collected at a hadal depth of 7,410 m in the Puerto Rico Trench of the Atlantic Ocean. Its minimum, optimum, and maximum growth pressures at 2°C were 1,020 atm hydrostatic pressure, respectively. At 10°C., all cardinal growth pressures shifted upwards about 200 atm, but at no tested pressure was the organism capable of growth at 15°C. Most rapid generation time, 7 h, was observed at 10°C and 925 atm. Selected taxonomic tests and a G+C % mol ratio of 45.7 indicate the strain belongs to the vibrioenteric group of bacteria. However, evolutionary tree and principal coordinates analyses, based on the ribonucleotide sequences of 5S ribosomal RNA from BNL-1 and other bacteria, indicate its distinction at the generic level from all but one member of this group, including other known barophiles. We recommend that a new genus, Colwellia gen. nov., be established and that the obligate barophile, strain BNL-1, be designated Colwellia hadaliensis , gen. nov. sp. nov. We further recommend the renaming of Vibrio psychroerythrus ATCC 27364, the organism with which BNL-1 shares most recent common ancestry, as Colwellia psychroerythrus comb. nov.

The Northeast Water Polynya as an Atmospheric Co2 Sink - a Seasonal Rectification Hypothesis

During the multidisciplinary ‘NEW92’ cruise of the United States Coast Guard Cutter (USCGC) Polar Sea to the recurrent Northeast Water (NEW) Polynya (77–81°N, 6–17°W; July–August 1992), total dissolved inorganic carbon and total alkalinity in the water column were measured with high precision to determine the quantitative impact of biological processes on the regional air-sea flux of carbon. Biological processes depleted the total inorganic carbon of summer surface waters by up to 2 mol C m−2 or about 3%. On a regional basis this depletion correlated with depth-integrated values of chlorophyll a, particulate organic carbon, and the inorganic nitrogen deficit. Replacement of this carbon through exchange with the atmosphere was stalled owing to the low wind speeds during the month of the cruise, although model calculations indicate that the depletion could be replenished by a few weeks of strong winds before ice forms in the autumn. These measurements and observations allowed formulation of a new hypothesis whereby seasonally ice-covered regions like the NEW Polynya promote a unique biologically and physically mediated “rectification” of the typical (ice free, low latitude) seasonal cycle of air-sea CO2 flux. The resulting carbon sink is consistent with other productivity estimates and represents an export of biologically cycled carbon either to local sediments or offshore. If this scenario is representative of seasonally ice-covered Arctic shelves, then the rectification process could provide a small, negative feedback to excess atmospheric CO2.

Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene.

Dramatic decreases in the extent of Arctic multiyear ice (MYI) suggest this environment may disappear as early as 2100, replaced by ecologically different first-year ice. To better understand the implications of this loss on microbial biodiversity, we undertook a detailed census of the microbial community in MYI at two sites near the geographic North Pole using parallel tag sequencing of the 16S rRNA gene. Although the composition of the MYI microbial community has been characterized by previous studies, microbial community structure has not been. Although richness was lower in MYI than in underlying surface water, we found diversity to be comparable using the Simpson and Shannons indices (for Simpson t=0.65, P=0.56; for Shannon t=0.25, P=0.84 for a Students t-test of mean values). Cyanobacteria, comprising 6.8% of reads obtained from MYI, were observed for the first time in Arctic sea ice. In addition, several low-abundance clades not previously reported in sea ice were present, including the phylum TM7 and the classes Spartobacteria and Opitutae. Members of Coraliomargarita, a recently described genus of the class Opitutae, were present in sufficient numbers to suggest niche occupation within MYI.