Bacterial community dynamics and activity in relation to dissolved organic matter availability during sea-ice formation in a mesocosm experiment

Peer reviewe

Mechanisms of microbial carbon sequestration in the ocean – future research directions

This paper reviews progress on understanding biological carbon sequestration in the ocean with special reference to the microbial formation and transformation of recalcitrant dissolved organic carbon (RDOC), the microbial carbon pump (MCP). We propose that RDOC is a concept with a wide continuum of recalcitrance. Most RDOC compounds maintain their levels of recalcitrance only in a specific environmental context (RDOCt). The ocean RDOC pool also contains compounds that may be inaccessible to microbes due to their extremely low concentration (RDOCc). This differentiation allows us to appreciate the linkage between microbial source and RDOC composition on a range of temporal and spatial scales. Analyses of biomarkers and isotopic records show intensive MCP processes in the Proterozoic oceans when the MCP could have played a significant role in regulating climate. Understanding the dynamics of the MCP in conjunction with the better constrained biological pump (BP) over geological timescales could help to predict future climate trends. Integration of the MCP and the BP will require new research approaches and opportunities. Major goals include understanding the interactions between particulate organic carbon (POC) and RDOC that contribute to sequestration efficiency, and the concurrent determination of the chemical composition of organic carbon, microbial community composition and enzymatic activity. Molecular biomarkers and isotopic tracers should be employed to link water column processes to sediment records, as well as to link present-day observations to paleo-evolution. Ecosystem models need to be developed based on empirical relationships derived from bioassay experiments and field investigations in order to predict the dynamics of carbon cycling along the stability continuum of POC and RDOC under potential global change scenarios. We propose that inorganic nutrient input to coastal waters may reduce the capacity for carbon sequestration as RDOC. The nutrient regime enabling maximum carbon storage from combined POC flux and RDOC formation should therefore be sought

Living on the edge: Biofilms developing in oscillating environmental conditions

For the first time, the densities and diversity of microorganisms developed on ocean gliders were investigated using flow cytometry and Illumina MiSeq sequencing of 16S and 18S rRNA genes. Ocean gliders are autonomous buoyancy-driven underwater vehicles, equipped with sensors continuously recording physical, chemical, and biological parameters. Microbial biofilms were investigated on unprotected parts of the glider and surfaces coated with base, biocidal and chitosan paints. Biofilms on the glider were exposed to periodical oscillations of salinity, oxygen, temperature, pressure, depth and light, due to periodic ascending and descending of the vehicle. Among the unprotected surfaces, the highest microbial abundance was observed on the bottom of the glider’s body, while the lowest density was recorded on the glider’s nose. Antifouling paints had the lowest densities of microorganisms. Multidimensional analysis showed that the microbial communities formed on unprotected parts of the glider were significantly different from those on biocidal paint and in seawater

Seasonal dynamics of active SAR11 ecotypes in the oligotrophic Northwest Mediterranean Sea

A seven-year oceanographic time series in NW Mediterranean surface waters was combined with pyrosequencing of ribosomal RNA (16S rRNA) and ribosomal RNA gene copies (16S rDNA) to examine the environmental controls on SAR11 ecotype dynamics and potential activity. SAR11 diversity exhibited pronounced seasonal cycles remarkably similar to total bacterial diversity. The timing of diversity maxima was similar across narrow and broad phylogenetic clades and strongly associated with deep winter mixing. Diversity minima were associated with periods of stratification that were low in nutrients and phytoplankton biomass and characterised by intense phosphate limitation (turnover time80%) by SAR11 Ia. A partial least squares (PLS) regression model was developed that could reliably predict sequence abundances of SAR11 ecotypes (Q2=0.70) from measured environmental variables, of which mixed layer depth was quantitatively the most important. Comparison of clade-level SAR11 rRNA:rDNA signals with leucine incorporation enabled us to partially validate the use of these ratios as an in-situ activity measure. However, temporal trends in the activity of SAR11 ecotypes and their relationship to environmental variables were unclear. The strong and predictable temporal patterns observed in SAR11 sequence abundance was not linked to metabolic activity of different ecotypes at the phylogenetic and temporal resolution of our study

Ocean currents shape the microbiome of Arctic marine sediments

Prokaryote communities were investigated on the seasonally stratified Alaska Beaufort Shelf (ABS). Water and sediment directly underlying water with origin in the Arctic, Pacific or Atlantic oceans were analyzed by pyrosequencing and length heterogeneity-PCR in conjunction with physicochemical and geographic distance data to determine what features structure ABS microbiomes. Distinct bacterial communities were evident in all water masses. Alphaproteobacteria explained similarity in Arctic surface water and Pacific derived water. Deltaproteobacteria were abundant in Atlantic origin water and drove similarity among samples. Most archaeal sequences in water were related to unclassified marine Euryarchaeota. Sediment communities influenced by Pacific and Atlantic water were distinct from each other and pelagic communities. Firmicutes and Chloroflexi were abundant in sediment, although their distribution varied in Atlantic and Pacific influenced sites. Thermoprotei dominated archaea in Pacific influenced sediments and Methanomicrobia dominated in methane-containing Atlantic influenced sediments. Length heterogeneity-PCR data from this study were analyzed with data from methane-containing sediments in other regions. Pacific influenced ABS sediments clustered with Pacific sites from New Zealand and Chilean coastal margins. Atlantic influenced ABS sediments formed another distinct cluster. Density and salinity were significant structuring features on pelagic communities. Porosity co-varied with benthic community structure across sites and methane did not. This study indicates that the origin of water overlying sediments shapes benthic communities locally and globally and that hydrography exerts greater influence on microbial community structure than the availability of methane

Biotic and abiotic retention, recycling and remineralization of metals in the ocean

Trace metals shape both the biogeochemical functioning and biological structure of oceanic provinces. Trace metal biogeochemistry has primarily focused on modes of external supply of metals from aeolian, hydrothermal, sedimentary and other sources. However, metals also undergo internal transformations such as abiotic and biotic retention, recycling and remineralization. The role of these internal transformations in metal biogeochemical cycling is now coming into focus. First, the retention of metals by biota in the surface ocean for days, weeks or months depends on taxon-specific metal requirements of phytoplankton, and on their ultimate fate: that is, viral lysis, senescence, grazing and/or export to depth. Rapid recycling of metals in the surface ocean can extend seasonal productivity by maintaining higher levels of metal bioavailability compared to the influence of external metal input alone. As metal-containing organic particles are exported from the surface ocean, different metals exhibit distinct patterns of remineralization with depth. These patterns are mediated by a wide range of physicochemical and microbial processes such as the ability of particles to sorb metals, and are influenced by the mineral and organic characteristics of sinking particles. We conclude that internal metal transformations play an essential role in controlling metal bioavailability, phytoplankton distributions and the subsurface resupply of metals

Catchment-scale biogeography of riverine bacterioplankton

Lotic ecosystems such as rivers and streams are unique in that they represent a continuum of both space and time during the transition from headwaters to the river mouth. As microbes have very different controls over their ecology, distribution and dispersion compared with macrobiota, we wished to explore biogeographical patterns within a river catchment and uncover the major drivers structuring bacterioplankton communities. Water samples collected across the River Thames Basin, UK, covering the transition from headwater tributaries to the lower reaches of the main river channel were characterised using 16S rRNA gene pyrosequencing. This approach revealed an ecological succession in the bacterial community composition along the river continuum, moving from a community dominated by Bacteroidetes in the headwaters to Actinobacteria-dominated downstream. Location of the sampling point in the river network (measured as the cumulative water channel distance upstream) was found to be the most predictive spatial feature; inferring that ecological processes pertaining to temporal community succession are of prime importance in driving the assemblages of riverine bacterioplankton communities. A decrease in bacterial activity rates and an increase in the abundance of low nucleic acid bacteria relative to high nucleic acid bacteria were found to correspond with these downstream changes in community structure, suggesting corresponding functional changes. Our findings show that bacterial communities across the Thames basin exhibit an ecological succession along the river continuum, and that this is primarily driven by water residence time rather than the physiochemical status of the river

Reconciliation of the carbon budget in the ocean’s twilight zone

Photosynthesis in the surface ocean produces approximately 100 gigatonnes of organic carbon per year, of which 5 to 15 per cent is exported to the deep ocean1, 2. The rate at which the sinking carbon is converted into carbon dioxide by heterotrophic organisms at depth is important in controlling oceanic carbon storage3. It remains uncertain, however, to what extent surface ocean carbon supply meets the demand of water-column biota; the discrepancy between known carbon sources and sinks is as much as two orders of magnitude4, 5, 6, 7, 8. Here we present field measurements, respiration rate estimates and a steady-state model that allow us to balance carbon sources and sinks to within observational uncertainties at the Porcupine Abyssal Plain site in the eastern North Atlantic Ocean. We find that prokaryotes are responsible for 70 to 92 per cent of the estimated remineralization in the twilight zone (depths of 50 to 1,000 metres) despite the fact that much of the organic carbon is exported in the form of large, fast-sinking particles accessible to larger zooplankton. We suggest that this occurs because zooplankton fragment and ingest half of the fast-sinking particles, of which more than 30 per cent may be released as suspended and slowly sinking matter, stimulating the deep-ocean microbial loop. The synergy between microbes and zooplankton in the twilight zone is important to our understanding of the processes controlling the oceanic carbon sink

Potential overestimation of community respiration in the western Pacific boundary ocean : what causes the putative net heterotrophy in oligotrophic systems?

Microbial metabolism is of great importance in affecting the efficiency of biological pump and global carbon cycles. However, the metabolic state of the oligotrophic ocean, the largest biome on Earth, remains contentious. We examined the planktonic and bacterial metabolism using in vitro incubations along the western Pacific boundary during September and October 2016. The integrated gross primary production (GPP) of the photic zone exhibited higher values in the region of 2°–8°N along 130°E and the western Luzon Strait, which is consistent with the regional variability of nutrients in the different ocean provinces. Spatially, the community respiration (CR) was less variable than the GPP and slightly exceeded the GPP at most of the sampling stations. Overall, the in vitro incubation results suggest a prevailing heterotrophic state in this region. A comparison of the metabolic rates from the in vitro incubations with recently published biogeochemical model results in the same region shows that our observed GPP values were close to those predicted by the model, but the measured CR was approximately 30% higher than the modeled values. We also found that most of the in vitro CR estimates were higher than the upper range of the empirical CR estimated from the sum of the contributions of the main trophic groups. Conversely, the estimates of the empirical CR support the rationality of the CR predicted by the biogeochemical model. In general, the results indicate that systematic net heterotrophy is more likely a result of the overestimation of CR measured by the light–dark bottle incubation experiments, although the exact cause of the methodological problem remains unknown