E.W. Maas's research while affiliated with Ministry for Primary Industries and other places

Due to a typesetting error, 25 rows were omitted from Table 3 in the original version of this Data Descriptor. These missing rows correspond to the following sample names:

Recent advances in understanding the ecology of marine systems have been greatly facilitated by the growing availability of metagenomic data, which provide information on the identity, diversity and functional potential of the microbial community in a particular place and time. Here we present a dataset comprising over 5 terabases of metagenomic data from 610 samples spanning diverse regions of the Atlantic and Pacific Oceans. One set of metagenomes, collected on GEOTRACES cruises, captures large geographic transects at multiple depths per station. The second set represents two years of time-series data, collected at roughly monthly intervals from 3 depths at two long-term ocean sampling sites, Station ALOHA and BATS. These metagenomes contain genomic information from a diverse range of bacteria, archaea, eukaryotes and viruses. The data’s utility is strengthened by the availability of extensive physical, chemical, and biological measurements associated with each sample. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of marine microbial ecosystems.

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.

Proteorhodopsin (PR) is a wide-spread protein found in many marine prokaryotes. PR allows for the potential conversion of solar energy to ATP, possibly assisting in cellular growth and survival during periods of high environmental stress. PR utilises either blue or green light through a single amino acid substitution. We incubated the PR-bearing bacterium Psychroflexus torquis 50 cm deep within Antarctic sea ice for 13 days, exposing cultures to diurnal fluctuations in light and temperature. Enhanced growth occurred most prominently in cultures incubated under irradiance levels of ∼50 μmol photons m(-2) s(-1), suggesting PR provides a strong selective advantage. In addition, cultures grown under blue light yielded over 5.5 times more live cells per photon compared to green-light incubations. Because P. torquis expresses an apparently 'green-shifted' PR gene variant, this finding infers that the spectral tuning of PR is more complex than previously thought. This study supports the theory that PR provides additional energy to bacteria under sub-optimal conditions, and raises several points of interest to be addressed by future research.The ISME Journal advance online publication, 19 May 2017; doi:10.1038/ismej.2017.65.

Extracellular bacterial enzymes play an important role in the degradation of organic matter in the surface ocean but are sensitive to changes in pH and temperature. This study tested the individual and combined effects of lower pH (-0.3) and warming (+3°C) projected for the year 2100 on bacterial abundance, process rates and diversity in plankton communities of differing composition from 4 locations east of New Zealand. Variation was observed in magnitude and temporal response between the different communities during 5 to 6 day incubations. Leucine aminopeptidase activity showed the strongest response, with an increase in potential activity under low pH alone and in combination with elevated temperature in 3 of 4 incubations. Temperature had a greater effect on bacterial cell numbers and protein synthesis, with stronger responses in the elevated temperature and combined treatments. However, the most common interactive effect between temperature and pH was antagonistic, with lower bacterial secondary production in the combined treatment relative to elevated temperature, and lower leucine aminopeptidase activity in the combined treatment relative to low pH. These results highlight the variability of responses to and interactions of environmental drivers, and the importance of considering these in experimental studies and prognostic models of microbial responses to climate change.

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 to 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 7–8 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.

Bacterial extracellular enzymes play a significant role in the degradation of labile organic matter and nutrient availability in the open ocean. Although bacterial production and extracellular enzymes may be affected by ocean acidification, few studies to date have considered the methodology used to measure enzyme activity and bacterial processes. This study investigated the potential artefacts in determining the response of bacterial growth and extracellular glucosidase and aminopeptidase activity to ocean acidification as well as the relative effects of three different acidification techniques. Tests confirmed that the observed effect of pH on fluorescence of artificial fluorophores, and the influence of the MCA fluorescent substrate on seawater sample pH, were both overcome by the use of Tris buffer. In experiments testing different acidification methods, bubbling with CO2 gas mixtures resulted in higher β-glucosidase activity and 15–40 % higher bacterial abundance, relative to acidification via gas-permeable silicon tubing and acid addition (HCl). Bubbling may stimulate carbohydrate degradation and bacterial growth, leading to the incorrect interpretation of the impacts of ocean acidification on organic matter cycling.

Bacterial extracellular enzymes play a significant role in the degradation of labile organic matter and nutrient availability in the open ocean. Although bacterial production and extracellular enzymes may be affected by ocean acidification, few studies to date have considered the methodology used to measure enzyme activity and bacterial processes. This study investigated the potential artefacts in determining the response of bacterial extracellular glucosidase and aminopeptidase to ocean acidification, and the relative effects of three different acidification techniques. Tests confirmed that the fluorescence of the artificial fluorophores was affected by pH, and that addition of MCA fluorescent substrate alters seawater pH. In experiments testing different acidification methods, bubbling with CO2 gas mixtures resulted in higher β-glucosidase activity relative to acidification by their introduction via gas-permeable silicon tubing, or by acid addition (HCl). In addition, bacterial numbers were 15–40 % higher with bubbling relative to seawater acidified with gas-permeable silicon tubing and HCl. Bubbling may lead to overestimation of carbohydrate degradation and bacterial abundance, and consequently incorrect interpretation of the impacts of ocean acidification on organic matter cycling.