Seasonal changes in planktonic bacterivory rates under the ice-covered coastal Arctic Ocean

Bacterivory was determined in surface waters of Franklin Bay, western Arctic, over a seasonal ice-covered period (winter-spring, 2003-2004). The objectives were to obtain information on the functioning of the microbial food web under the ice, during winter (from 21 December 2003 to 21 March 2004) and during spring (from 22 March 2004 to 29 May 2004), and to test whether bacterial losses would increase after the increase in bacterial production following the spring phytoplankton bloom. Chl a concentrations ranged from 0.04 to 0.36 mu g L(-1), increasing in March and reaching a peak in April. Bacterial biomass showed no consistent trend for the whole period, and protist biomass followed a pattern similar to that of Chl a. Bacterial production increased 1 week after Chl a concentrations started to increase, while bacterivory rates increased very slightly. Average bacterivory rates in winter (0.16 +/- 0.07 mu g C L(-1) d(-1)) were not significantly different from those in spring (0.29 +/- 0.24 mu g C L(-1) d(-1)). Average bacterial production, on the other hand, was similar to bacterivory rates in winter (0.19 +/- 0.38 mu g C L(-1) d(-1)), but higher than bacterivory in spring (0.93 +/- 0.28 mu g C L(-1) d(-1)). Therefore, bacterial production was controlled by grazers during winter and by substrate concentration in spring

Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection

Microbiota provide their hosts with a range of beneficial services, including defense from external pathogens. However, host-associated microbial communities themselves can act as a source of opportunistic pathogens depending on the environment. Marine poikilotherms and their microbiota are strongly influenced by temperature, but experimental studies exploring how temperature affects the interactions between both parties are rare. To assess the effects of temperature, temperature stress and infection on diversity, composition and dynamics of the hemolymph microbiota of Pacific oysters (Crassostrea gigas), we conducted an experiment in a fully-crossed, three-factorial design, in which the temperature acclimated oysters (8 or 22 °C) were exposed to temperature stress and to experimental challenge with a virulent Vibrio sp. Strain. We monitored oyster survival and repeatedly collected hemolymph of dead and alive animals to determine the microbiome composition by 16s rRNA gene amplicon pyrosequencing. We found that the microbial dynamics and composition of communities in healthy animals (including infection survivors) were significantly affected by temperature and temperature stress, but not by infection. The response was mediated by changes in the incidence and abundance of operational taxonomic units (OTUs) and accompanied by little change at higher taxonomic levels, indicating dynamic stability of the hemolymph microbiome. Dead and moribund oysters, on the contrary, displayed signs of community structure disruption, characterized by very low diversity and proliferation of few OTUs. We can therefore link short-term responses of host-associated microbial communities to abiotic and biotic factors and assess the potential feedback between microbiota dynamics and host survival during disease

Sustaining rare marine microorganisms: macroorganisms as repositories and dispersal agents of microbial diversity

Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism-microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares, which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members

Roadmap for naming uncultivated Archaea and Bacteria

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity

Biological turnover of DMS, DMSP and DMSO in contrasting open-sea waters

11 pages, 2 figures, 3 tablesSpeciation and turnover of the methylated sulfur compounds dimethyl sulfide (DMS), dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) were studied in waters of the open western Mediterranean, the near-coastal North Sea and the subpolar North Atlantic, with chlorophyll a concentrations spanning 2 orders of magnitude (0.12 to 13 μg 1-1>). Particulate DMSP (DMSP(p): 5 to 340 nM) was the predominant pool in most waters. Dissolved and particulate dimethyl sulfoxide were alsofound at significant concentrations (DMSO(d): 2 to 25 nM, DMSO(p): 3 to 16 nM). Biological DMSP consumption rates were estimated from the time course of total (dissolved + particulate) DMSP Concentration in dark incubations Dimethyl sulfide production and consumption rates were determined by the 'inhibitor addition' method. High DMS production and consumption rates were found during a bloom of Phaeocystis sp. in North Sea waters. In all samples, turnover time constants for total DMSP and DMS were of the same order, ranging from 0.7 to 5.4 and from 0.3 to 2.1 d, respectively. DMS formation was the fate for 9 to 96% of the DMSP consumed. Use of chloroform as an inhibitor gave estimates of DMS production and consumption rates approximately 70% higher than those obtained with dimethyl disulfide and dimethyl selenide. In some incubation experiments, the time course of DMSO concentration has been followed along with DMS and DMSP for the first time. Evidence for active biological cycling (production and consumption) of DMSO in seawater is presentedPeer Reviewe

Differential response of grazing and bacterial heterotrophic production to experimental warming in Antarctic waters

Narrow annual ranges of temperature characterize polar waters. Consequently, small increases in temperature could significantly affect the metabolic processes of marine microorganisms. We investigated the response of bacterial heterotrophic production (BHP) and grazing rates to small temperature changes in 3 zones near the western Antarctic Peninsula-Bransfield and Gerlache Straits, and Bellingshausen Sea-during December 2002. We performed 8 grazing experiments with water samples collected from depths where chlorophyll a (chl a) concentration was maximum, and incubated the samples at ambient temperature and at -1, 1, 2 and 5 degrees C. We expected that grazing would increase in parallel with BHP at increasing temperatures; however, temperature differentially affected these 2 microbial activities. Thus, grazing rates increased maximally at temperatures <= 2 degrees C, except in 1 station in the Gerlache Strait, while BHP increased maximally at temperatures <= 2 degrees C, except in 1 station in the Bellingshausen Sea. The percentage of grazed bacteria to BHP at the highest experimental temperatures was low (56 +/- 19%) in the Gerlache Strait, high (395 +/- 137%) in the Bransfield Strait and approximately balanced (97 +/- 24%) in the Bellingshausen Sea. This suggests that differential microbial processes in each zone at increasing temperatures will also depend on the autochthonous community. The present study contributes to the understanding of the variability of polar biogeochemical fluxes, and may aid in predicting the response of microorganisms in future scenarios with local and seasonal changes in temperature

Spatial patterns of bacterial richness and evenness in the NW Mediterranean Sea explored by pyrosequencing of the 16S rRNA

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 Microbila Ecology 61 (2010): 221-233, doi:10.3354/ame01484.Due to analytical limitations, patterns of richness and evenness of microbes are scarce in the current literature. The newest and powerful pyrosequencing technology may solve this issue by sampling thousands of sequences from the same community. We conducted a study of diversity along a horizontal transect (ca. 120 km) and a depth profile (surface to bottom at ca. 2000 m) in the northwestern Mediterranean Sea, using this technology on the V6 region of the 16S rDNA gene and analyzed patterns of richness and evenness of marine free-living bacterial communities. A total of 201605 tag sequences were obtained from the 10 samples considered and clustered according to their similarity in 1200 operational taxonomic units (OTUs) per sample on average. We found a parallel decrease in richness and evenness from coast to offshore and from bottom to surface. We also observed a predominance of a few OTUs in each sample, while ca. 50% of all OTUs were found as singletons, which indicated that the community structures differed dramatically between sites despite the relative proximity and the physical connectivity between the samples. Despite these differences, using the 300 most abundant OTUs only was sufficient to obtain the same clustering of samples as with the complete dataset. Finally, both richness and evenness were negatively correlated with bacterial biomass and heterotrophic production.The Modivus cruise was supported by the Spanish MICINN project MODIVUS (CTM2005-04795/ MAR). Additional work was supported by a Spanish MICINN grant GEMMA (CTM2007-63753-C02-01/MAR)