Elizabeth W. Maas

Pole-to-pole biogeography of surface and deep marine bacterial communities

The Antarctic and Arctic regions offer a unique opportunity to test factors shaping biogeography of marine microbial communities because these regions are geographically far apart, yet share similar selection pressures. Here, we report a comprehensive comparison of bacterioplankton diversity between polar oceans, using standardized methods for pyrosequencing the V6 region of the small subunit ribosomal (SSU) rRNA gene. Bacterial communities from lower latitude oceans were included, providing a global perspective. A clear difference between Southern and Arctic Ocean surface communities was evident, with 78% of operational taxonomic units (OTUs) unique to the Southern Ocean and 70% unique to the Arctic Ocean. Although polar ocean bacterial communities were more similar to each other than to lower latitude pelagic communities, analyses of depths, seasons, and coastal vs. open waters, the Southern and Arctic Ocean bacterioplankton communities consistently clustered separately from each other. Coastal surface Southern and Arctic Ocean communities were more dissimilar from their respective open ocean communities. In contrast, deep ocean communities differed less between poles and lower latitude deep waters and displayed different diversity patterns compared with the surface. In addition, estimated diversity (Chao1) for surface and deep communities did not correlate significantly with latitude or temperature. Our results suggest differences in environmental conditions at the poles and different selection mechanisms controlling surface and deep ocean community structure and diversity. Surface bacterioplankton may be subjected to more short-term, variable conditions, whereas deep communities appear to be structured by longer water-mass residence time and connectivity through ocean circulation.

Proteorhodopsin-Bearing Bacteria in Antarctic Sea Ice

ABSTRACT Proteorhodopsins (PRs) are widespread bacterial integral membrane proteins that function as light-driven proton pumps. Antarctic sea ice supports a complex community of autotrophic algae, heterotrophic bacteria, viruses, and protists that are an important food source for higher trophic levels in ice-covered regions of the Southern Ocean. Here, we present the first report of PR-bearing bacteria, both dormant and active, in Antarctic sea ice from a series of sites in the Ross Sea using gene-specific primers. Positive PR sequences were generated from genomic DNA at all depths in sea ice, and these sequences aligned with the classes Alphaproteobacteria, Gammaproteobacteria, and Flavobacteria. The sequences showed some similarity to previously reported PR sequences, although most of the sequences were generally distinct. Positive PR sequences were also observed from cDNA reverse transcribed from RNA isolated from sea ice samples. This finding indicates that these sequences were generated from metabolically active cells and suggests that the PR gene is functional within sea ice. Both blue-absorbing and green-absorbing forms of PRs were detected, and only a limited number of blue-absorbing forms were found and were in the midsection of the sea ice profile in this study. Questions still remain regarding the proteins ecological functions, and ultimately, field experiments will be needed to establish the ecological and functional role of PRs in the sea ice ecosystem.

Archaeal diversity revealed in Antarctic sea ice

Abstract Archaea, once thought to be only extremophiles, are now known to be abundant in most environments. They can predominate in microbial communities and be significantly involved in many global biogeochemical cycles. However, Archaea have not been reported in Antarctic sea ice. Our understanding of the ecology of Antarctic sea ice prokaryotes is still in its infancy but this information is important if we are to understand their diversity, adaptations and biogeochemical roles in Antarctic systems. We detected Archaea in sea ice at two sampling sites taken from three subsequent years using conserved 16S rRNA gene archaeal primers and PCR. Archaeal abundance was measured using quantitative PCR and community diversity was investigated by sequencing cloned 16S rRNA gene PCR products. Archaea in Antarctic sea ice were found to be in low abundance consisting of ≤ 6.6% of the prokaryotic community. The majority, 90.8% of the sequences, clustered with the recently described phylum Thaumarchaeota, one group closely clustered with the ammonia-oxidizing Candidatus Nitrosopumilus maritimus. The remainder of the clones grouped with the Euryarchaeota.

Temporal changes in particle-associated microbial communities after interception by nonlethal sediment traps.

Using marine sediment traps (named RESPIRE for REspiration of Sinking Particles In the subsuRface ocEan) designed to collect sinking particles and associated microbial communities in situ, we collected and incubated marine aggregates/particles in the southern Pacific Ocean from separate phytoplankton bloom events in situ. We determined the phylogenetic affiliation for the microorganisms growing on aggregates by pyrosequencing partial 16S rRNA gene amplicons. Water column samples were also collected and sequenced for comparison between sinking-particle-associated and planktonic bacterial communities. Statistically significant differences were found between the water column and sediment trap bacteria. Relative abundances of Pelagibacter sp. and multiple members of the Flavobacteria, Actinobacteria, and α-Proteobacteria were elevated in water column samples, while trap samples contained members of the Roseobacter clade of α-Proteobacteria in high relative abundances. Our findings indicated that rapid changes - within 24 h of collection - occurred to the microbial community associated with aggregates from either bloom type. There was a little change in the bacterial assemblage after the initial 24-h incubation period. The most abundant early colonizer was a Sulfitobacter sp. This study provides further evidence that Roseobacters are rapid colonizers of marine aggregates and that colonization can occur on short timescales. This study further demonstrates that particle origin may be insignificant regarding the heterotrophic bacterial population that degrades them.

Patterns of deep-sea genetic connectivity in the New Zealand region: implications for management of benthic ecosystems.

Patterns of genetic connectivity are increasingly considered in the design of marine protected areas (MPAs) in both shallow and deep water. In the New Zealand Exclusive Economic Zone (EEZ), deep-sea communities at upper bathyal depths (<2000 m) are vulnerable to anthropogenic disturbance from fishing and potential mining operations. Currently, patterns of genetic connectivity among deep-sea populations throughout New Zealand’s EEZ are not well understood. Using the mitochondrial Cytochrome Oxidase I and 16S rRNA genes as genetic markers, this study aimed to elucidate patterns of genetic connectivity among populations of two common benthic invertebrates with contrasting life history strategies. Populations of the squat lobster Munida gracilis and the polychaete Hyalinoecia longibranchiata were sampled from continental slope, seamount, and offshore rise habitats on the Chatham Rise, Hikurangi Margin, and Challenger Plateau. For the polychaete, significant population structure was detected among distinct populations on the Chatham Rise, the Hikurangi Margin, and the Challenger Plateau. Significant genetic differences existed between slope and seamount populations on the Hikurangi Margin, as did evidence of population differentiation between the northeast and southwest parts of the Chatham Rise. In contrast, no significant population structure was detected across the study area for the squat lobster. Patterns of genetic connectivity in Hyalinoecia longibranchiata are likely influenced by a number of factors including current regimes that operate on varying spatial and temporal scales to produce potential barriers to dispersal. The striking difference in population structure between species can be attributed to differences in life history strategies. The results of this study are discussed in the context of existing conservation areas that are intended to manage anthropogenic threats to deep-sea benthic communities in the New Zealand region.

Ferrioxamine Siderophores Detected amongst Iron Binding Ligands Produced during the Remineralization of Marine Particles

The microbial degradation of marine particles is an important process in the remineralization of nutrients including iron. As part of the GEOTRACES process study (FeCycle II), we conducted incubation experiments with marine particles obtained from 30 and 100 m depth at two stations during austral spring in the subtropical waters east of the North Island of New Zealand. The particles were collected using in-situ pumps, and comprised mainly of suspended and slow sinking populations along with associated attached heterotrophic bacteria. In treatments with live bacteria, increasing concentrations of Fe binding ligands were observed with an average stability constant of logKFeL,Fe3+ = 21.11±0.37 for station 1 and 20.89±0.25 for station 2. The ligand release rates varied between 2.54 and 11.8 pmol L-1 d-1 (calculated for ambient seawater particle concentration) and were similar to those found in two Southern Ocean subsurface studies from ~110 m depths in subpolar and polar waters. Dissolved iron (DFe) was released at a rate between 0.33 and 2.09 pmol Fe L-1 d-1 with a column integrated (30 -100 m) flux of 107 and 58 nmol Fe m-2 day-1 at station 1 and 2, respectively. Given a mixed layer DFe inventory of ~48 µmol m-2 and ~4 µmol m-2 at the time of sampling for station 1 and 2, this will therefore result in a DFe residence time of 1.2 and 0.18 years, assuming particle remineralization was the only source of iron in the mixed layer. The DFe release rates calculated were comparable to those found in the previously mentioned study of Southern Ocean water masses. Fe-binding ligand producing bacteria (CAS positive) abundance was found to increase throughout the duration of the experiment of 7 to 8 days. For the first time ferrioxamine type siderophores, including the well-known ferrioxamine B and G, have been quantified using chemical assays and LC-ESI-MS. Our subtropical study corroborates prior reports from the Southern Ocean of particle remineralization being an important source of DFe and ligands, and adds unprecedented detail by revealing that siderophores are probably an important component of the ligands released into subsurface waters during particle remineralisation.

Cryopreservation of marine thraustochytrids (Labyrinthulomycetes).

In this research, the viability of three marine thraustochytrid isolates (fungoid protists) (WSG05, W15 and WH3) were investigated after freezing in liquid nitrogen. Five cryopreservative combinations containing horse serum, glycerol and dimethylsulfide (Me(2)SO) were used. The thraustochytrids were assessed directly after removal from liquid nitrogen and cell concentration measured for 10 days post-thawing. Results indicated that a combination of horse serum and Me(2)SO were the most effective cryoprotectants for each of the strains tested. Glycerol was only successful in producing growth in one of the strains once thawed. The protocols developed and tested in this study may have further application for cryopreserving other isolates in this class.

Bacterial abundance, processes and diversity responses to acidification at a coastal CO2 vent.

Shallow CO2 vents are used as natural laboratories to study biological responses to ocean acidification, and so it is important to determine whether pH is the primary driver of bacterial processes and community composition, or whether other variables associated with vent water have a significant influence. Water from a CO2 vent (46 m, Bay of Plenty, New Zealand) was compared to reference water from an upstream control site, and also to control water acidified to the same pH as the vent water. After 84 h, both vent and acidified water exhibited higher potential bulk water and cell-specific glucosidase activity relative to control water, whereas cell-specific protease activities were similar. However, bulk vent water glucosidase activity was double that of the acidified water, as was bacterial secondary production in one experiment, suggesting that pH was not the only factor affecting carbohydrate hydrolysis. In addition, there were significant differences in bacterial community composition in the vent water relative to the control and acidified water after 84 h, including the presence of extremophiles which may influence carbohydrate degradation. This highlights the importance of characterizing microbial processes and community composition in CO2 vent emissions, to confirm that they represent robust analogues for the future acidified ocean.

Modification of an algal culture medium for sustained growth of a saxitoxin-producing isolate of Alexandrium minutum

In order to study saxitoxin (STX) production bymicro-algae in the laboratory, a defined algal culture medium which supports optimum growth over a longtime-period is a requirement. In the development of such a medium, a number of modifications were made to a standard algal culture medium (GP) and growth of a STX-producing isolate of Alexandrium minutum in the different formulations was assessed by measuring maximum cell densities and mean generation times (MGT). All experiments were carried out under controlled conditions in an aerobic atmosphere with increased CO2. Whilst maximum cell densities in the different modifications were similar, the MGT was significantly shortened by the addition of Tris buffer and the trace metals strontium, selenium and molybdenum. Replacement of natural with artificial seawater and removal of soil extract did not adversely affect algal growth. Five of the six media formulations supported the growth of A. minutumover a 9-month period.

Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments

Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.