Single-cell physiological structure and growth rates of heterotrophic bacteria in a temperate estuary (Waquoit Bay, Massachusetts)

Author Posting. © American Society of Limnology and Oceanography, 2011. This article is posted here by permission of American Society of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 56 (2011): 37-48, doi:10.4319/lo.2011.56.1.0037.Flow cytometric determinations of membrane integrity, nucleic acid content, and respiratory activity were combined with dilution cultures in Waquoit Bay Estuary (Massachusetts) to estimate specific growth rates of total, live, high (HNA), and low (LNA) nucleic acid content and actively respiring (CTC+) cells. Bacterial abundance ranged from 106 to 107 cells mL-1, with live cells generally contributing > 85% to total numbers, 42-82% HNA cells, and 3-36% CTC+ cells. Specific growth rates (µ) from all physiological groups were positively correlated, but they showed different temperature dependences, with activation energies ranging from 0.28 (live) to 0.97 eV (LNA). The µ values of live cells (0.14-2.40 d-1) were similar to those of total bacteria (0.06-1.53 d-1). LNA bacteria were not dormant but showed positive growth in most experiments, although HNA cells greatly outgrew LNA cells (µ ranges of 0.28-2.26 d-1 vs. 0-0.69 d-1), and CTC+ cells showed the highest values (0.12-2.65 d-1). Positive correlations of HNA bacteria µ with total and phytoplankton-derived dissolved organic carbon support the previously hypothesized strong bottom-up control of HNA cells. Bacterial production estimated from leucine incorporation and empirical conversion factors agreed well with estimates based on growth rates. HNA cells were always responsible for the largest share of bacterial production in the estuary. The contribution of CTC+ cells significantly increased with temperature in the 7-27°C range, reaching values of 40% at temperatures higher than 20°C.This study was supported by the Spanish Ministry of Science and Innovation (MICINN) sabbatical stay program (to X.A.G.M.), National Science Foundation Office of Polar Programs grant 0823101 to H.W.D., and by the Marine Biological Laboratory

Heterotrophic bacterioplankton responses in coral- and algae-dominated Red Sea reefs show they might benefit from future regime shift

In coral reefs, dissolved organic matter (DOM) cycling is a critical process for sustaining ecosystem functioning. However, global and local stressors have caused persistent shifts from coral- to algae-dominated benthic communities. The influence of such phase shifts on DOM nature and its utilization by heterotrophic bacterioplankton remains poorly studied. Every second month for one year, we retrieved seawater samples enriched in DOM produced by coral- and algae-dominated benthic communities in a central Red Sea reef during a full annual cycle. Seawater incubations were conducted in the laboratory under in situ temperature and light conditions by inoculating enriched DOM samples with bacterial assemblages collected in the surrounding waters. Dissolved organic carbon (DOC) concentrations were higher in the warmer months (May-September) in both communities, resulting in higher specific growth rates and bacterial growth efficiencies (BGE). However, these high summer values were significantly enhanced in algal-DOM relative to coral-DOM, suggesting the potential for bacterioplankton biomass increase in reefs with algae replacing healthy coral cover under warmer conditions. The potential exacerbation of heterotrophic bacterial activity in the ongoing widespread regime shift from coral- to algae-dominated communities may have detrimental consequences for the overall health of tropical coral reefs. (C) 2020 The Authors. Published by Elsevier B.V.Peer reviewe

Factors controlling the community structure of picoplankton in contrasting marine environments

The effect of inorganic nutrients on planktonic assemblages has traditionally relied on concentrations rather than estimates of nutrient supply. We combined a novel dataset of hydrographic properties, turbulent mixing, nutrient concentration, and picoplankton community composition with the aims of (i) quantifying the role of temperature, light, and nitrate fluxes as factors controlling the distribution of autotrophic and heterotrophic picoplankton subgroups, as determined by flow cytometry, and (ii) describing the ecological niches of the various components of the picoplankton community. Data were collected at 97 stations in the Atlantic Ocean, including tropical and subtropical open-ocean waters, the northwestern Mediterranean Sea, and the Galician coastal upwelling system of the northwest Iberian Peninsula. A generalized additive model (GAM) approach was used to predict depth-integrated biomass of each picoplankton subgroup based on three niche predictors: sea surface temperature, averaged daily surface irradiance, and the transport of nitrate into the euphotic zone, through both diffusion and advection. In addition, niche overlap among different picoplankton subgroups was computed using nonparametric kernel density functions. Temperature and nitrate supply were more relevant than light in predicting the biomass of most picoplankton subgroups, except for Prochlorococcus and low-nucleic-acid (LNA) prokaryotes, for which irradiance also played a significant role. Nitrate supply was the only factor that allowed the distinction among the ecological niches of all autotrophic and heterotrophic picoplankton subgroups. Prochlorococcus and LNA prokaryotes were more abundant in warmer waters ( \u3e 20°C) where the nitrate fluxes were low, whereas Synechococcus and high-nucleic-acid (HNA) prokaryotes prevailed mainly in cooler environments characterized by intermediate or high levels of nitrate supply. Finally, the niche of picoeukaryotes was defined by low temperatures and high nitrate supply. These results support the key role of nitrate supply, as it not only promotes the growth of large phytoplankton, but it also controls the structure of marine picoplankton communities

High summer temperatures amplify functional differences between coral- and algae-dominated reef communities

Shifts from coral to algal dominance are expected to increase in tropical coral reefs as a result of anthropogenic disturbances. The consequences for key ecosystem functions such as primary productivity, calcification, and nutrient recycling are poorly understood, particularly under changing environmental conditions. We used a novel in situ incubation approach to compare functions of coral- and algae-dominated communities in the central Red Sea bimonthly over an entire year. In situ gross and net community primary productivity, calcification, dissolved organic carbon fluxes, dissolved inorganic nitrogen fluxes, and their respective activation energies were quantified to describe the effects of seasonal changes. Overall, coral-dominated communities exhibited 30% lower net productivity and 10 times higher calcification than algae-dominated communities. Estimated activation energies indicated a higher thermal sensitivity of coral-dominated communities. In these communities, net productivity and calcification were negatively correlated with temperature (>40% and >65% reduction, respectively, with +5 degrees C increase from winter to summer), whereas carbon losses via respiration and dissolved organic carbon release more than doubled at higher temperatures. In contrast, algae-dominated communities doubled net productivity in summer, while calcification and dissolved organic carbon fluxes were unaffected. These results suggest pronounced changes in community functioning associated with coral-algal phase shifts. Algae-dominated communities may outcompete coral-dominated communities because of their higher productivity and carbon retention to support fast biomass accumulation while compromising the formation of important reef framework structures. Higher temperatures likely amplify these functional differences, indicating a high vulnerability of ecosystem functions of coral-dominated communities to temperatures even below coral bleaching thresholds. Our results suggest that ocean warming may not only cause but also amplify coral-algal phase shifts in coral reefs.Peer reviewe

Nutrient pollution enhances productivity and framework dissolution in algae- but not in coral-dominated reef communities

Ecosystem services provided by coral reefs may be susceptible to the combined effects of benthic species shifts and anthropogenic nutrient pollution, but related field studies are scarce. We thus investigated in situ how dissolved inorganic nutrient enrichment, maintained for two months, affected community-wide biogeochemical functions of intact coral- and degraded algae-dominated reef patches in the central Red Sea. Results from benthic chamber incubations revealed 87% increased gross productivity and a shift from net calcification to dissolution in algae-dominated communities after nutrient enrichment, but the same processes were unaffected by nutrients in neighboring coral communities. Both community types changed from net dissolved organic nitrogen sinks to sources, but the increase in net release was 56% higher in algae-dominated communities. Nutrient pollution may, thus, amplify the effects of community shifts on key ecosystem services of coral reefs, possibly leading to a loss of structurally complex habitats with carbonate dissolution and altered nutrient recycling.Peer reviewe

Nutrient pollution enhances productivity and framework dissolution in algae- but not in coral-dominated reef communities

Ecosystem services provided by coral reefs may be susceptible to the combined effects of benthic species shifts and anthropogenic nutrient pollution, but related field studies are scarce. We thus investigated in situ how dissolved inorganic nutrient enrichment, maintained for two months, affected community-wide biogeochemical functions of intact coral- and degraded algae-dominated reef patches in the central Red Sea. Results from benthic chamber incubations revealed 87% increased gross productivity and a shift from net calcification to dissolution in algae-dominated communities after nutrient enrichment, but the same processes were unaffected by nutrients in neighboring coral communities. Both community types changed from net dissolved organic nitrogen sinks to sources, but the increase in net release was 56% higher in algae-dominated communities. Nutrient pollution may, thus, amplify the effects of community shifts on key ecosystem services of coral reefs, possibly leading to a loss of structurally complex habitats with carbonate dissolution and altered nutrient recycling.This work was supported by KAUST baseline funding to BHJ and by grant Wi 2677/9-1 from the German Research Foundation (DFG) to C

Molecular analyses of protists in long-term observation programmes—current status and future perspectives

Protists (microbial eukaryotes) are diverse, major components of marine ecosystems, and are fundamental to ecosystem services. In the last 10 years, molecular studies have highlighted substantial novel diversity in marine systems including sequences with no taxonomic context. At the same time, many known protists remain without a DNA identity. Since the majority of pelagic protists are too small to identify by light microscopy, most are neither comprehensively or regularly taken into account, particularly in Long-term Ecological Research Sites. This potentially undermines the quality of research and the accuracy of predictions about biological species shifts in a changing environment. The ICES Working Group for Phytoplankton and Microbial Ecology conducted a questionnaire survey in 2013–2014 on methods and identification of protists using molecular methods plus a literature review of protist molecular diversity studies. The results revealed an increased use of high-throughput sequencing methods and a recognition that sequence data enhance the overall datasets on protist species composition. However, we found only a few long-term molecular studies and noticed a lack of integration between microscopic and molecular methods. Here, we discuss and put forward recommendations to improve and make molecular methods more accessible to Long-term Ecological Research Site investigators

Total and phytoplankton mediated bottom-up control of bacterioplankton change with temperature in NE Atlantic shelf waters

Author Posting. © Inter-Research, 2010. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Aquatic Microbial Ecology 58 (2010): 229-239, doi:10.3354/ame01374.The regulation of heterotrophic bacterial growth by resource supply (bottom-up control) was temperature-dependent in our analysis of data obtained during 2006 in the euphotic layer of the southern Bay of Biscay (NE Atlantic) continental shelf. The dataset was split into 2 subgroups using 16°C as the boundary between warm and cool waters based on differences in associated physico-chemical conditions, e.g. inorganic nutrient limitation at higher temperatures. The linear regressions between bacterial biomass (BB) and leucine incorporation rates (LIR) were significantly positive in both temperature regimes, thus indicating similar total bottom-up control, albeit with a slightly higher slope in warm waters (0.33 vs. 0.22). However, the relationship of LIR with phytoplankton biomass (chl a), which is an indicator of bottom-up control that is mediated by phytoplankton, was only significant in waters below 16°C. The analysis of bimonthly variations in the BB-LIR and LIR-chl a correlations indicated that the strength of total bottom-up control significantly increased while the role of phytoplankton in supplying DOM to bacteria diminished with mean temperatures over the 12 to 19°C range, suggesting a seasonal switch in the major source of substrates used by bacteria. We show that the abundance of cells with relatively high nucleic acid content (HNA), which are hypothesized to be the most active ones, was positively associated with bacterial production and specific growth rates in cool but not in warm conditions. These results suggest that HNA bacteria are good predictors of bulk activity and production in temperate ecosystems only when the community relies principally on phytoplankton substrates for growth and metabolism.X.A.G.M. was partially supported by a sabbatical grant at the MBL from the Spanish Ministry of Education and Science (MEC) and A.C.-D. received an FPI research training predoctoral fellowhip. This work was supported by the time-series project RADIALES from the Instituto Espanol de Oceanografia (IEO)

Towards a better understanding of microbial carbon flux in the sea

Author Posting. © Inter-Research, 2008. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Aquatic Microbial Ecology 53 (2008): 21-38, doi:10.3354/ame01230.We now have a relatively good idea of how bulk microbial processes shape the cycling of organic matter and nutrients in the sea. The advent of the molecular biology era in microbial ecology has resulted in advanced knowledge about the diversity of marine microorganisms, suggesting that we might have reached a high level of understanding of carbon fluxes in the oceans. However, it is becoming increasingly clear that there are large gaps in the understanding of the role of bacteria in regulating carbon fluxes. These gaps may result from methodological as well as conceptual limitations. For example, should bacterial production be measured in the light? Can bacterial production conversion factors be predicted, and how are they affected by loss of tracers through respiration? Is it true that respiration is relatively constant compared to production? How can accurate measures of bacterial growth efficiency be obtained? In this paper, we discuss whether such questions could (or should) be addressed. Ongoing genome analyses are rapidly widening our understanding of possible metabolic pathways and cellular adaptations used by marine bacteria in their quest for resources and struggle for survival (e.g. utilization of light, acquisition of nutrients, predator avoidance, etc.). Further, analyses of the identity of bacteria using molecular markers (e.g. subgroups of Bacteria and Archaea) combined with activity tracers might bring knowledge to a higher level. Since bacterial growth (and thereby consumption of DOC and inorganic nutrients) is likely regulated differently in different bacteria, it will be critical to learn about the life strategies of the key bacterial species to achieve a comprehensive understanding of bacterial regulation of C fluxes. Finally, some processes known to occur in the microbial food web are hardly ever characterized and are not represented in current food web models. We discuss these issues and offer specific comments and advice for future research agendas.Our work was supported by the following grants: NSF grant 0217282 (H.D.), Spanish MEC grant MODIVUS (J.M.G.), the Swedish Science Council (J.P.), the IEO time-series RADIALES programme (X.A.G.M.), the Earth and Life Science Division of the Dutch Science Foundation, ARCHIMEDES project, #835.20.023 (G.J.H.)