A latitudinal diversity gradient in planktonic marine bacteria

Response of bacterial metabolic activity to riverine dissolved organic carbon and exogenous viruses in estuarine and coastal waters: implications for CO2 emission

A cross-transplant experiment between estuarine water and seawater was conducted to examine the response of bacterial metabolic activity to riverine dissolved organic carbon (DOC) input under virus-rich and virus-free conditions, as well as to exogenous viruses. Riverine DOC input increased bacterial production significantly, but not bacterial respiration (BR) because of its high lability. The bioavailable riverine DOC influenced bulk bacterial respiration in two contrasting ways; it enhanced the bulk BR by stimulating bacterial growth, but simultaneously reduced the cell-specific BR due to its high lability. As a result, there was little stimulation of the bulk BR by riverine DOC. This might be partly responsible for lower CO₂ degassing fluxes in estuaries receiving high sewage-DOC that is highly labile. Viruses restricted microbial decomposition of riverine DOC dramatically by repressing the growth of metabolically active bacteria. Bacterial carbon demand in the presence of viruses only accounted for 7–12% of that in the absence of viruses. Consequently, a large fraction of riverine DOC was likely transported offshore to the shelf. In addition, marine bacteria and estuarine bacteria responded distinctly to exogenous viruses. Marine viruses were able to infect estuarine bacteria, but not as efficiently as estuarine viruses, while estuarine viruses infected marine bacteria as efficiently as marine viruses. We speculate that the rapid changes in the viral community due to freshwater input destroyed the existing bacteria-virus relationship, which would change the bacterial community composition and affect the bacterial metabolic activity and carbon cycling in this estuary.

Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors

Holobionts are species-specific associations between macro- and microorganisms. On coral reefs, the benthic coverage of coral and algal holobionts varies due to natural and anthropogenic forcings. Different benthic macroorganisms are predicted to have specific microbiomes. In contrast, local environmental factors are predicted to select for specific metabolic pathways in microbes. To reconcile these two predictions, we hypothesized that adaptation of microbiomes to local conditions is facilitated by the horizontal transfer of genes responsible for specific metabolic capabilities. To test this hypothesis, microbial metagenomes were sequenced from 22 coral reefs at 11 Line Islands in the central Pacific that together span a wide range of biogeochemical and anthropogenic influences. Consistent with our hypothesis, the percent cover of major benthic functional groups significantly correlated with particular microbial taxa. Reefs with higher coral cover had a coral microbiome with higher abundances of Alphaproteobacteria (such as Rhodobacterales and Sphingomonadales), whereas microbiomes of algae-dominated reefs had higher abundances of Gammaproteobacteria (such as Alteromonadales, Pseudomonadales, and Vibrionales), Betaproteobacteria, and Bacteriodetes. In contrast to taxa, geography was the strongest predictor of microbial community metabolism. Microbial communities on reefs with higher nutrient availability (e.g., equatorial upwelling zones) were enriched in genes involved in nutrient-related metabolisms (e.g., nitrate and nitrite ammonification, Ton/Tol transport, etc.). On reefs further from the equator, microbes had more genes encoding chlorophyll biosynthesis and photosystems I/II. These results support the hypothesis that core microbiomes are determined by holobiont macroorganisms, and that those core taxa adapt to local conditions by selecting for advantageous metabolic genes.

Patterns of Microbially Driven Carbon Cycling in the Ocean: Links between Extracellular Enzymes and Microbial Communities

Heterotrophic microbial communities play a central role in the marine carbon cycle. They are active in nearly all known environments, from the surface to the deep ocean, in the sediments, and from the equator to the Poles. In order to process complex organic matter, these communities produce extracellular enzymes of the correct structural specificity to hydrolyze substrates to sizes sufficiently small for uptake. Extracellular enzymatic hydrolysis thus initiates heterotrophic carbon cycling. Our knowledge of the enzymatic capabilities of microbial communities in the ocean is still underdeveloped. Recent studies, however, suggest that there may be large-scale patterns of enzymatic function in the ocean, patterns of community function that may be connected to emerging patterns of microbial community composition. Here I review some of these large-scale contrasts in microbial enzyme activities, between high-latitude and temperate surface ocean waters, contrasts between inshore and offshore waters, changes with depth gradients in the ocean, and contrasts between the water column and underlying sediments. These contrasting patterns are set in the context of recent studies of microbial communities and patterns of microbial biogeography. Focusing on microbial community function as well as composition and potential should yield clearer understanding of the factors driving carbon cycling in the ocean.

Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds

Marine microorganisms continue to be a source of structurally and biologically novel compounds with potential use in the biotechnology industry. The unique physiochemical properties of the marine environment (such as pH, pressure, temperature, osmolarity) and uncommon functional groups (such as isonitrile, dichloroimine, isocyanate, and halogenated functional groups) are frequently found in marine metabolites. These facts have resulted in the production of bioactive substances with different properties than those found in terrestrial habitats. In fact, the marine environment contains a relatively untapped reservoir of bioactivity. Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts. The combination of these advanced techniques with traditional techniques, together with the use of dereplication strategies to eliminate known compounds, provides a powerful tool in the discovery of novel marine bioactive compounds. This review outlines and discusses the emerging strategies for the biodiscovery of these bioactive compounds.

Composition and enzymatic function of particle-associated and free-living bacteria: a coastal/offshore comparison

We compared the function and composition of free-living and particle-associated microbial communities at an inshore site in coastal North Carolina and across a depth profile on the Blake Ridge (offshore). Hydrolysis rates of six different polysaccharide substrates were compared for particle-associated (>3 μm) and free-living (<3 to 0.2 μm) microbial communities. The 16S rRNA- and rDNA-based clone libraries were produced from the same filters used to measure hydrolysis rates. Particle-associated and free-living communities resembled one another; they also showed similar enzymatic hydrolysis rates and substrate preferences. All six polysaccharides were hydrolyzed inshore. Offshore, only a subset was hydrolyzed in surface water and at depths of 146 and 505 m; just three polysaccharides were hydrolyzed at 505 m. The spectrum of bacterial taxa changed more subtly between inshore and offshore surface waters, but changed greatly with depth offshore. None of the OTUs occurred at all sites: 27 out of the 28 major OTUs defined in this study were found either exclusively in a surface or in a mid-depth/bottom water sample. This distinction was evident with both 16S rRNA and rDNA analyses. At the offshore site, despite the low community overlap, bacterial communities maintained a degree of functional redundancy on the whole bacterial community level with respect to hydrolysis of high-molecular-weight substrates.

The pattern of change in the abundances of specific bacterioplankton groups is consistent across different nutrient-enriched habitats in Crete

A common source of disturbance for coastal aquatic habitats is nutrient enrichment through anthropogenic activities. Although the water column bacterioplankton communities in these environments have been characterized in some cases, changes in α-diversity and/or the abundances of specific taxonomic groups across enriched habitats remain unclear. Here, we investigated the bacterial community changes at three different nutrient-enriched and adjacent undisturbed habitats along the north coast of Crete, Greece: a fish farm, a closed bay within a town with low water renewal rates, and a city port where the level of nutrient enrichment and the trophic status of the habitat were different. Even though changes in α-diversity were different at each site, we observed across the sites a common change pattern accounting for most of the community variation for five of the most abundant bacterial groups: a decrease in the abundance of the Pelagibacteraceae and SAR86 and an increase in the abundance of the Alteromonadaceae, Rhodobacteraceae, and Cryomorphaceae in the impacted sites. The abundances of the groups that increased and decreased in the impacted sites were significantly correlated (positively and negatively, respectively) with the total heterotrophic bacterial counts and the concentrations of dissolved organic carbon and/or dissolved nitrogen and chlorophyll α, indicating that the common change pattern was associated with nutrient enrichment. Our results provide an in situ indication concerning the association of specific bacterioplankton groups with nutrient enrichment. These groups could potentially be used as indicators for nutrient enrichment if the pattern is confirmed over a broader spatial and temporal scale by future studies.

Diversity of rare and abundant bacteria in surface waters of the Southern Adriatic Sea

Bacteria are fundamental players in the functioning of the ocean, yet relatively little is known about the diversity of bacterioplankton assemblages and the factors shaping their spatial distribution. We investigated the diversity and community composition of bacterioplankton in surface waters of the Southern Adriatic sub-basin (SAd) in the Mediterranean Sea, across an environmental gradient from coastal to offshore stations. Bacterioplankton diversity was investigated using a whole-assemblage genetic fingerprinting technique (Automated Ribosomal Intergenic Spacer Analysis, ARISA) coupled with 16S rDNA amplicon pyrosequencing. The main physico-chemical variables showed clear differences between coastal and offshore stations, with the latter displaying generally higher temperature, salinity and oxygen content. Bacterioplankton richness was higher in coastal than offshore waters. Bacterial community composition (BCC) differed significantly between coastal and offshore waters, and appeared to be influenced by temperature (explaining up to 30% of variance) and by the trophic state. Pyrosequencing evidenced dominance of Alphaproteobacteria (SAR11 cluster), uncultured Gammaproteobacteria (Rhodobacteraceae) and Cyanobacteria (Synechococcus). Members of the Bacteroidetes phylum were also abundant, and accounted for 25% in the station characterized by the higher organic carbon availability. Bacterioplankton assemblages included a few dominant taxa and a very large proportion (85%) of rare (<0.1%) bacteria, the vast majority of which was unique to each sampling station. The first detailed census of bacterioplankton taxa in the SAd sub-basin, performed using next generation sequencing, indicates that assemblages are highly heterogeneous, spatially structured according to the environmental conditions, and comprise a large number of rare taxa. The high turnover diversity, particularly evident at the level of the rare taxa, suggests to direct future investigations toward larger spatial or temporal scales, to better understand the role of bacterioplankton in the ecosystem functioning and the biogeochemistry of the basin.

Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

Despite microbes' key roles in driving biogeochemical cycles, the mechanism of microbe-mediated feedbacks to global changes remains elusive. Recently, soil transplant has been successfully established as a proxy to simulate climate changes, as the current trend of global warming coherently causes range shifts toward higher latitudes. Four years after southward soil transplant over large transects in China, we found that microbial functional diversity was increased, in addition to concurrent changes in microbial biomass, soil nutrient content and functional processes involved in the nitrogen cycle. However, soil transplant effects could be overridden by maize cropping, which was attributed to a negative interaction. Strikingly, abundances of nitrogen and carbon cycle genes were increased by these field experiments simulating global change, coinciding with higher soil nitrification potential and carbon dioxide (CO2) efflux. Further investigation revealed strong correlations between carbon cycle genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycle genes and nitrification. These findings suggest that changes of soil carbon and nitrogen cycles by soil transplant and cropping were predictable by measuring microbial functional potentials, contributing to a better mechanistic understanding of these soil functional processes and suggesting a potential to incorporate microbial communities in greenhouse gas emission modeling.

A trait based perspective on the biogeography of common and abundant marine bacterioplankton clades

Marine microbial communities provide much of the energy upon which all higher trophic levels depend, particularly in open-ocean and oligotrophic systems, and play a pivotal role in biogeochemical cycling. How and why species are distributed in the global oceans, and whether net ecosystem function can be accurately predicted from community composition are fundamental questions for marine scientists. Many of the most abundant clades of marine bacteria, including the Prochlorococcus, Synechococcus, SAR11, SAR86 and Roseobacter, have a very broad, if not a cosmopolitan distribution. However this is not reflected in an underlying genetic identity. Rather, widespread distribution in these organisms is achieved by the existence of closely related but discrete ecotypes that display niche adaptations. Closely related ecotypes display specific nutritional or energy generating mechanisms and are adapted to different physical parameters including temperature, salinity, and hydrostatic pressure. Furthermore, biotic phenomena such as selective grazing and viral loss contribute to the success or failure of ecotypes allowing some to compete effectively in particular marine provinces but not in others. An additional layer of complexity is added by ocean currents and hydrodynamic specificity of water body masses that bound microbial dispersal and immigration. These vary in space and time with respect to intensity and direction, making the definition of large biogeographic provinces problematic. A deterministic theory aimed at understanding how all these factors shape microbial life in the oceans can only proceed through analysis of microbial traits, rather than pure phylogenetic assessments. Trait based approaches seek mechanistic explanations for the observed temporal and spatial patterns. This review will present successful recent advances in phylogenetic and trait based biogeographic analyses in some of the most abundant marine taxa.

Large-scale ichthyoplankton and water mass distribution along the South Brazil Shelf

Ichthyoplankton is an essential component of pelagic ecosystems, and environmental factors play an important role in determining its distribution. We have investigated simultaneous latitudinal and cross-shelf gradients in ichthyoplankton abundance to test the hypothesis that the large-scale distribution of fish larvae in the South Brazil Shelf is associated with water mass composition. Vertical plankton tows were collected between 21°27' and 34°51'S at 107 stations, in austral late spring and early summer seasons. Samples were taken with a conical-cylindrical plankton net from the depth of chlorophyll maxima to the surface in deep stations, or from 10 m from the bottom to the surface in shallow waters. Salinity and temperature were obtained with a CTD/rosette system, which provided seawater for chlorophyll-a and nutrient concentrations. The influence of water mass on larval fish species was studied using Indicator Species Analysis, whereas environmental effects on the distribution of larval fish species were analyzed by Distance-based Redundancy Analysis. Larval fish species were associated with specific water masses: in the north, Sardinella brasiliensis was found in Shelf Water; whereas in the south, Engraulis anchoita inhabited the Plata Plume Water. At the slope, Tropical Water was characterized by the bristlemouth Cyclothone acclinidens. The concurrent analysis showed the importance of both cross-shelf and latitudinal gradients on the large-scale distribution of larval fish species. Our findings reveal that ichthyoplankton composition and large-scale spatial distribution are determined by water mass composition in both latitudinal and cross-shelf gradients.

Fine-scale spatial patterns in bacterial community composition and function within freshwater ponds

The extent to which non-host-associated bacterial communities exhibit small-scale biogeographic patterns in their distribution remains unclear. Our investigation of biogeography in bacterial community composition and function compared samples collected across a smaller spatial scale than most previous studies conducted in freshwater. Using a grid-based sampling design, we abstracted 100+ samples located between 3.5 and 60 m apart within each of three alpine ponds. For every sample, variability in bacterial community composition was monitored using a DNA-fingerprinting methodology (automated ribosomal intergenic spacer analysis) whereas differences in bacterial community function (that is, carbon substrate utilisation patterns) were recorded from Biolog Ecoplates. The exact spatial position and dominant physicochemical conditions (for example, pH and temperature) were simultaneously recorded for each sample location. We assessed spatial differences in bacterial community composition and function within each pond and found that, on average, community composition or function differed significantly when comparing samples located >20 m apart within any pond. Variance partitioning revealed that purely spatial variation accounted for more of the observed variability in both bacterial community composition and function (range: 24-38% and 17-39%) than the combination of purely environmental variation and spatially structured environmental variation (range: 17-32% and 15-20%). Clear spatial patterns in bacterial community composition, but not function were observed within ponds. We therefore suggest that some of the observed variation in bacterial community composition is functionally 'redundant'. We confirm that distinct bacterial communities are present across unexpectedly small spatial scales suggesting that populations separated by distances of >20 m may be dispersal limited, even within the highly continuous environment of lentic water.

Faster speciation and reduced extinction in the tropics contribute to the Mammalian latitudinal diversity gradient

Jonathan Rolland and colleagues show that the gradient of increased mammalian diversity towards the tropics is driven by both faster speciation and reduced extinction.

The increase in species richness from the poles to the tropics, referred to as the latitudinal diversity gradient, is one of the most ubiquitous biodiversity patterns in the natural world. Although understanding how rates of speciation and extinction vary with latitude is central to explaining this pattern, such analyses have been impeded by the difficulty of estimating diversification rates associated with specific geographic locations. Here, we use a powerful phylogenetic approach and a nearly complete phylogeny of mammals to estimate speciation, extinction, and dispersal rates associated with the tropical and temperate biomes. Overall, speciation rates are higher, and extinction rates lower, in the tropics than in temperate regions. The diversity of the eight most species-rich mammalian orders (covering 92% of all mammals) peaks in the tropics, except that of the Lagomorpha (hares, rabbits, and pikas) reaching a maxima in northern-temperate regions. Latitudinal patterns in diversification rates are strikingly consistent with these diversity patterns, with peaks in species richness associated with low extinction rates (Primates and Lagomorpha), high speciation rates (Diprotodontia, Artiodactyla, and Soricomorpha), or both (Chiroptera and Rodentia). Rates of range expansion were typically higher from the tropics to the temperate regions than in the other direction, supporting the “out of the tropics” hypothesis whereby species originate in the tropics and disperse into higher latitudes. Overall, these results suggest that differences in diversification rates have played a major role in shaping the modern latitudinal diversity gradient in mammals, and illustrate the usefulness of recently developed phylogenetic approaches for understanding this famous yet mysterious pattern.

Why are there more species in the tropics? This question has fascinated ecologists and evolutionary biologists for decades, generating hundreds of hypotheses, yet basic questions remain: Are rates of speciation higher in the tropics? Are rates of extinction higher in temperate regions? Do the tropics act as a source of diversity for temperate regions? We estimated rates of speciation, extinction, and range expansion associated with mammals living in tropical and temperate regions, using an almost complete mammalian phylogeny. Contrary to what has been suggested before for this class of vertebrates, we found that diversification rates are strikingly consistent with diversity patterns, with latitudinal peaks in species richness being associated with high speciation rates, low extinction rates, or both, depending on the mammalian order (rodents, bats, primates, etc.). We also found evidence for an asymmetry in range expansion, with more expansion “out of” than “into” the tropics. Taken together, these results suggest that tropical regions are not only a reservoir of biodiversity, but also the main place where biodiversity is generated.

Humboldt's spa: microbial diversity is controlled by temperature in geothermal environments

Over 200 years ago Alexander von Humboldt (1808) observed that plant and animal diversity peaks at tropical latitudes and decreases toward the poles, a trend he attributed to more favorable temperatures in the tropics. Studies to date suggest that this temperature-diversity gradient is weak or nonexistent for Bacteria and Archaea. To test the impacts of temperature as well as pH on bacterial and archaeal diversity, we performed pyrotag sequencing of 16S rRNA genes retrieved from 165 soil, sediment and biomat samples of 36 geothermal areas in Canada and New Zealand, covering a temperature range of 7.5-99 °C and a pH range of 1.8-9.0. This represents the widest ranges of temperature and pH yet examined in a single microbial diversity study. Species richness and diversity indices were strongly correlated to temperature, with R(2) values up to 0.62 for neutral-alkaline springs. The distributions were unimodal, with peak diversity at 24 °C and decreasing diversity at higher and lower temperature extremes. There was also a significant pH effect on diversity; however, in contrast to previous studies of soil microbial diversity, pH explained less of the variability (13-20%) than temperature in the geothermal samples. No correlation was observed between diversity values and latitude from the equator, and we therefore infer a direct temperature effect in our data set. These results demonstrate that temperature exerts a strong control on microbial diversity when considered over most of the temperature range within which life is possible.

Biodiversity and multifunctionality in a microbial community: a novel theoretical approach to quantify functional redundancy

Ecosystems have a limited buffering capacity of multiple ecosystem functions against biodiversity loss (i.e. low multifunctional redundancy). We developed a novel theoretical approach to evaluate multifunctional redundancy in a microbial community using the microbial genome database (MBGD) for comparative analysis. In order to fully implement functional information, we defined orthologue richness in a community, each of which is a functionally conservative evolutionary unit in genomes, as an index of community multifunctionality (MF). We constructed a graph of expected orthologue richness in a community (MF) as a function of species richness (SR), fit the power function to SR (i.e. MF = cSR^a), and interpreted the higher exponent a as the lower multifunctional redundancy. Through a microcosm experiment, we confirmed that MF defined by orthologue richness could predict the actual multiple functions. We simulated random and non-random community assemblages using full genomic data of 478 prokaryotic species in the MBGD, and determined that the exponent in microbial communities ranged from 0.55 to 0.75. This exponent range provided a quantitative estimate that a 6.6–8.9% loss limit in SR occurred in a microbial community for an MF reduction no greater than 5%, suggesting a non-negligible initial loss effect of microbial diversity on MF.

Patterns of extracellular enzyme activities and microbial metabolism in an Arctic fjord of Svalbard and in the northern Gulf of Mexico: contrasts in carbon processing by pelagic microbial communities

The microbial community composition of polar and temperate ocean waters differs substantially, but the potential functional consequences of these differences are largely unexplored. We measured bacterial production, glucose metabolism, and the abilities of microbial communities to hydrolyze a range of polysaccharides in an Arctic fjord of Svalbard (Smeerenburg Fjord), and thus to initiate remineralization of high-molecular weight organic matter. We compared these data with similar measurements previously carried out in the northern Gulf of Mexico in order to investigate whether differences in the spectrum of enzyme activities measurable in Arctic and temperate environments are reflected in “downstream” aspects of microbial metabolism (metabolism of monomers and biomass production). Only four of six polysaccharide substrates were hydrolyzed in Smeerenburg Fjord; all were hydrolyzed in the upper water column of the Gulf. These patterns are consistent on an interannual basis. Bacterial protein production was comparable at both locations, but the pathways of glucose utilization differed. Glucose incorporation rate constants were comparatively higher in Svalbard, but glucose respiration rate constants were higher in surface waters of the Gulf. As a result, at the time of sampling ca. 75% of the glucose was incorporated into biomass in Svalbard, but in the northern Gulf of Mexico most of the glucose was respired to CO₂. A limited range of enzyme activities is therefore not a sign of a dormant community or one unable to further process substrates resulting from extracellular enzymatic hydrolysis. The ultimate fate of carbohydrates in marine waters, however, is strongly dependent upon the specific capabilities of heterotrophic microbial communities in these disparate environments.

Patterns and drivers of bacterial α- and β-diversity across vertical profiles from surface to subsurface sediments

We investigated the patterns and drivers of bacterial α- and β-diversity, along with viral and prokaryotic abundance and the carbon production rates, in marine surface and subsurface sediments (down to 1 m depth) in two habitats: vegetated sediments (seagrass meadow) and non-vegetated sediments. Prokaryotic abundance and production decreased with depth in the sediment, but cell-specific production rates and the virus-to-prokaryote ratio increased, highlighting unexpectedly high activity in the subsurface. The highest diversity was observed in vegetated sediments. Bacterial β-diversity between sediment horizons was high, and only a minor number of taxa was shared between surface and subsurface layers. Viruses significantly contributed to explain α- and β-diversity patterns. Despite potential limitations due to the only use of fingerprinting techniques, this study indicates that the coastal subsurface host highly active and diversified bacterial assemblages, that subsurface cells are more active than expected and that viruses promote β-diversity and stimulate bacterial metabolism in subsurface layers. The limited number of taxa shared between habitats, and between surface and subsurface sediment horizons, suggests that future investigations of the shallow subsurface will provide insights into the census of bacterial diversity, and the comprehension of the patterns and drivers of prokaryotic diversity in marine ecosystems.

Analytical tools and databases for metagenomics in the next-generation sequencing era

Metagenomics has become one of the indispensable tools in microbial ecology for the last few decades, and a new revolution in metagenomic studies is now about to begin, with the help of recent advances of sequencing techniques. The massive data production and substantial cost reduction in next-generation sequencing have led to the rapid growth of metagenomic research both quantitatively and qualitatively. It is evident that metagenomics will be a standard tool for studying the diversity and function of microbes in the near future, as fingerprinting methods did previously. As the speed of data accumulation is accelerating, bioinformatic tools and associated databases for handling those datasets have become more urgent and necessary. To facilitate the bioinformatics analysis of metagenomic data, we review some recent tools and databases that are used widely in this field and give insights into the current challenges and future of metagenomics from a bioinformatics perspective.

Global marine bacterial diversity peaks at high latitudes in winter

Genomic approaches to characterizing bacterial communities are revealing significant differences in diversity and composition between environments. But bacterial distributions have not been mapped at a global scale. Although current community surveys are way too sparse to map global diversity patterns directly, there is now sufficient data to fit accurate models of how bacterial distributions vary across different environments and to make global scale maps from these models. We apply this approach to map the global distributions of bacteria in marine surface waters. Our spatially and temporally explicit predictions suggest that bacterial diversity peaks in temperate latitudes across the world's oceans. These global peaks are seasonal, occurring 6 months apart in the two hemispheres, in the boreal and austral winters. This pattern is quite different from the tropical, seasonally consistent diversity patterns observed for most macroorganisms. However, like other marine organisms, surface water bacteria are particularly diverse in regions of high human environmental impacts on the oceans. Our maps provide the first picture of bacterial distributions at a global scale and suggest important differences between the diversity patterns of bacteria compared with other organisms.

Strong seasonality and interannual recurrence in marine myovirus communities

The temporal community dynamics and persistence of different viral types in the marine environment are still mostly obscure. Polymorphism of the major capsid protein gene, g23, was used to investigate the community composition dynamics of T4-like myoviruses in a North Atlantic fjord for a period of 2 years. A total of 160 unique operational taxonomic units (OTUs) were identified by terminal restriction fragment length polymorphism (TRFLP) of the gene g23. Three major community profiles were identified (winter-spring, summer, and autumn), which resulted in a clear seasonal succession pattern. These seasonal transitions were recurrent over the 2 years and significantly correlated with progression of seawater temperature, Synechococcus abundance, and turbidity. The appearance of the autumn viral communities was concomitant with the occurrence of prominent Synechococcus blooms. As a whole, we found a highly dynamic T4-like viral community with strong seasonality and recurrence patterns. These communities were unexpectedly dominated by a group of persistently abundant viruses.

Estimation of hydrocarbon biodegradation rates in marine environments: a critical review of the Q10 approach

Offshore oil & gas industry is moving exploration and production activities into Arctic and deep water regions. Governmental regulations require environmental impact assessments before operations to evaluate the possible effects of accidental oil releases. These are often performed by numerical fate models, like the Oil Spill Contingency and Response (OSCAR) model, which has become an industry standard in Norway. In this model, biodegradation rates are adjusted to local conditions by temperature compensation according to a Q10 approach. Q10 is the multiplier by which rates of enzymatic reactions increase at a 10 °C temperature rise. Herein, this Q10 approach implemented in the OSCAR model is investigated based on published data and novel obtained results. Overall, biodegradation rate predictions calculated by temperature compensation are found to be questionable, and choosing one universal Q10 value is considered not feasible. The high variation in Q10 values is herein attributed to indirect effects of temperature.

Microbial habitat connectivity across spatial scales and hydrothermal temperature gradients at Guaymas Basin

The Guaymas Basin (Gulf of California) hydrothermal vent area is known as a dynamic and hydrothermally vented sedimentary system, where the advection and production of a variety of different metabolic substrates support a high microbial diversity and activity in the seafloor. The main objective of our study was to explore the role of temperature and other environmental factors on community diversity, such as the presence of microbial mats and seafloor bathymetry within one hydrothermally vented field of 200 × 250 m dimension. In this field, temperature increased strongly with sediment depth reaching the known limit of life within a few decimeters. Potential sulfate reduction rate as a key community activity parameter was strongly affected by in situ temperature and sediment depth, declining from high rates of 1–5 μmol ml⁻¹ d⁻¹ at the surface to the detection limit below 5 cm sediment depth, despite the presence of sulfate and hydrocarbons. Automated Ribosomal Intergenic Spacer Analysis yielded a high-resolution fingerprint of the dominant members of the bacterial community. Our analyses showed strong temperature and sediment depth effects on bacterial cell abundance and Operational Taxonomic Units (OTUs) number, both declining by more than one order of magnitude below the top 5 cm of the sediment surface. Another fraction of the variation in diversity and community structure was explained by differences in the local bathymetry and spatial position within the vent field. Nevertheless, more than 80% of all detected OTUs were shared among the different temperature realms and sediment depths, after being classified as cold (T < 10°C), medium (10°C ≤ T < 40°C) or hot (T ≥ 40°C) temperature conditions, with significant OTU overlap with the richer surface communities. Overall, this indicates a high connectivity of benthic bacterial habitats in this dynamic and heterogeneous marine ecosystem influenced by strong hydrothermalism.

Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight

Time-series are critical to understanding long-term natural variability in the oceans. Bacterial communities in the euphotic zone were investigated for over a decade at the San Pedro Ocean Time-series station (SPOT) off southern California. Community composition was assessed by Automated Ribosomal Intergenic Spacer Analysis (ARISA) and coupled with measurements of oceanographic parameters for the surface ocean (0-5 m) and deep chlorophyll maximum (DCM, average depth ≈ 30 m). SAR11 and cyanobacterial ecotypes comprised typically more than one-third of the measured community; diversity within both was temporally variable, although a few operational taxonomic units (OTUs) were consistently more abundant. Persistent OTUs, mostly Alphaproteobacteria (SAR11 clade), Actinobacteria and Flavobacteria, tended to be abundant, in contrast to many rarer yet intermittent and ephemeral OTUs. Association networks revealed potential niches for key OTUs from SAR11, cyanobacteria, SAR86 and other common clades on the basis of robust correlations. Resilience was evident by the average communities drifting only slightly as years passed. Average Bray-Curtis similarity between any pair of dates was ≈ 40%, with a slight decrease over the decade and obvious near-surface seasonality; communities 8-10 years apart were slightly more different than those 1-4 years apart with the highest rate of change at 0-5 m between communities <4 years apart. The surface exhibited more pronounced seasonality than the DCM. Inter-depth Bray-Curtis similarities repeatedly decreased as the water column stratified each summer. Environmental factors were better predictors of shifts in community composition than months or elapsed time alone; yet, the best predictor was community composition at the other depth (that is, 0-5 m versus DCM).

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

Planktonic bacteria dominate surface ocean biomass and influence global biogeochemical processes, but remain poorly characterized owing to difficulties in cultivation. Using large-scale single cell genomics, we obtained insight into the genome content and biogeography of many bacterial lineages inhabiting the surface ocean. We found that, compared with existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, and are depleted in guanine and cytosine, noncoding nucleotides, and genes encoding transcription, signal transduction, and noncytoplasmic proteins. These findings provide strong evidence that genome streamlining and oligotrophy are prevalent features among diverse, free-living bacterioplankton, whereas existing laboratory cultures consist primarily of copiotrophs. The apparent ubiquity of metabolic specialization and mixotrophy, as predicted from single cell genomes, also may contribute to the difficulty in bacterioplankton cultivation. Using metagenome fragment recruitment against single cell genomes, we show that the global distribution of surface ocean bacterioplankton correlates with temperature and latitude and is not limited by dispersal at the time scales required for nucleotide substitution to exceed the current operational definition of bacterial species. Single cell genomes with highly similar small subunit rRNA gene sequences exhibited significant genomic and biogeographic variability, highlighting challenges in the interpretation of individual gene surveys and metagenome assemblies in environmental microbiology. Our study demonstrates the utility of single cell genomics for gaining an improved understanding of the composition and dynamics of natural microbial assemblages.

Phylogenetic and morphologic complexity of giant sulphur bacteria

The large sulphur bacteria, first discovered in the early nineteenth century, include some of the largest bacteria identified to date. Individual cells are often visible to the unaided eye and can reach 750 μm in diameter. The cells usually feature light-refracting inclusions of elemental sulphur and a large internal aqueous vacuole, which restricts the cytoplasm to the outermost periphery. In some taxa, it has been demonstrated that the vacuole can also serve for the storage of high millimolar concentrations of nitrate. Over the course of the past two centuries, a wide range of morphological variation within the family Beggiatoaceae has been found. However, representatives of this clade are frequently recalcitrant to current standard microbiological techniques, including 16S rRNA gene sequencing and culturing, and a reliable classification of these bacteria is often complicated. Here we present a summary of the efforts made and achievements accomplished in the past years, and give perspectives for investigating the heterogeneity and possible evolutionary developments in this extraordinary group of bacteria.

Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin

Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (ρ=-0.664) and residence time (ρ=0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, and Prochlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments.

Naphthalene biodegradation in temperate and arctic marine microcosms

Naphthalene, the smallest polycyclic aromatic hydrocarbon (PAH), is found in abundance in crude oil, its major source in marine environments. PAH removal occurs via biodegradation, a key process determining their fate in the sea. Adequate estimation of PAH biodegradation rates is essential for environmental risk assessment and response planning using numerical models such as the oil spill contingency and response (OSCAR) model. Using naphthalene as a model compound, biodegradation rate, temperature response and bacterial community composition of seawaters from two climatically different areas (North Sea and Arctic Ocean) were studied and compared. Naphthalene degradation was followed by measuring oxygen consumption in closed bottles using the OxiTop(®) system. Microbial communities of untreated and naphthalene exposed samples were analysed by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing. Three times higher naphthalene degradation rate coefficients were observed in arctic seawater samples compared to temperate, at all incubation temperatures. Rate coefficients at in situ temperatures were however, similar (0.048 day(-1) for temperate and 0.068 day(-1) for arctic). Naphthalene biodegradation rates decreased with similar Q10 ratios (3.3 and 3.5) in both seawaters. Using the temperature compensation method implemented in the OSCAR model, Q10 = 2, biodegradation in arctic seawater was underestimated when calculated from the measured temperate k1 value, showing that temperature difference alone could not predict biodegradation rates adequately. Temperate and arctic untreated seawater communities were different as revealed by pyrosequencing. Geographic origin of seawater affected the community composition of exposed samples.

A meta-analysis of changes in bacterial and archaeal communities with time

Ecologists have long studied the temporal dynamics of plant and animal communities with much less attention paid to the temporal dynamics exhibited by microbial communities. As a result, we do not know if overarching temporal trends exist for microbial communities or if changes in microbial communities are generally predictable with time. Using microbial time series assessed via high-throughput sequencing, we conducted a meta-analysis of temporal dynamics in microbial communities, including 76 sites representing air, aquatic, soil, brewery wastewater treatment, human- and plant-associated microbial biomes. We found that temporal variability in both within- and between-community diversity was consistent among microbial communities from similar environments. Community structure changed systematically with time in less than half of the cases, and the highest rates of change were observed within ranges of 1 day to 1 month for all communities examined. Microbial communities exhibited species–time relationships (STRs), which describe the accumulation of new taxa to a community, similar to those observed previously for plant and animal communities, suggesting that STRs are remarkably consistent across a broad range of taxa. These results highlight that a continued integration of microbial ecology into the broader field of ecology will provide new insight into the temporal patterns of microbial and ‘macro'-bial communities alike.

Intra- and intergenomic variation of ribosomal RNA operons in concurrent Alteromonas macleodii strains

Biodiversity estimates based on ribosomal operon sequence diversity rely on the premise that a sequence is characteristic of a single specific taxon or operational taxonomic unit (OTU). Here, we have studied the sequence diversity of 14 ribosomal RNA operons (rrn) contained in the genomes of two isolates (five operons in each genome) and four metagenomic fosmids, all from the same seawater sample. Complete sequencing of the isolate genomes and the fosmids establish that they represent strains of the same species, Alteromonas macleodii, with average nucleotide identity (ANI) values >97 %. Nonetheless, we observed high levels of intragenomic heterogeneity (i.e., variability between operons of a single genome) affecting multiple regions of the 16S and 23S rRNA genes as well as the internally transcribed spacer 1 (ITS-1) region. Furthermore, the ribosomal operons exhibited intergenomic heterogeneity (i.e., variability between operons located in separate genomes) in each of these regions, compounding the variability. Our data reveal the extensive heterogeneity observed in natural populations of A. macleodii at a single point in time and support the idea that distinct lineages of A. macleodii exist in the deep Mediterranean. These findings highlight the potential of rRNA fingerprinting methods to misrepresent species diversity while simultaneously failing to recognize the ecological significance of individual strains.

Latitudinal diversity of sea anemones (Cnidaria: Actiniaria)

We sought to determine if the global distribution of sea anemones (cnidarian order Actiniaria) conforms to the classic pattern of biogeography--taxon richness at the equator with attenuation toward the poles--a pattern that is derived almost entirely from data on terrestrial plants and animals. We plotted the empirical distribution of species occurrences in 10° bands of latitude based on published information, then, using the Chao2 statistic, inferred the completeness of that inventory. We found the greatest species richness of sea anemones at 30-40° N and S, with lower numbers at tropical latitudes and the fewest species in polar areas. The Chao2 statistic allowed us to infer that the richness pattern we found is not due to particularly poor knowledge of tropical sea anemones. No 10° band of latitude has less than 60% of the theoretical number of species known, but for only about half of them could we reject the null hypothesis (P = 0.05) that information is complete; anemone diversity is best documented at high latitudes. We infer that the 1089 valid species currently known constitute about 70% of the theoretical total of about 1500 species of Actiniaria. The distribution pattern of sea anemone species resembles that of planktonic foraminiferans and benthic marine algae, although planktonic bacteria, marine bivalves, and shallow and deep scleractinian corals show the terrestrial pattern of equatorial richness attenuating with latitude. Sea anemone species richness is complementary to that of scleractinian corals at many scales; our findings affirm it at the global scale.

Bacterioplankton communities turn unstable and become small under increased temperature and nutrient-enriched conditions

The stability of microbial community composition under different environmental conditions is an important part of microbial ecology, but has not been investigated in such depth before. In this study, we investigated the composition of the bacterioplankton community composition (BCC) and its stability under different temperatures (15, 25 and 35 °C, respectively) and nutrient conditions (control vs. nitrogen- and phosphorus-enriched) in aquatic microcosms. The BCC was analysed using denaturing gradient gel electrophoresis of the bacterial 16S rRNA gene, followed by cloning and sequence analysis. BCC in the microcosms significantly changed under different temperature and nutrient conditions. Based on the results from clone libraries, ecological diversification were observed within two ubiquitous and dominant genera, Methylophilus and Polynucleobacter, under different temperature and nutrient conditions. Putative ultramicrobacteria, which included Actinobacteria, Polynucleobacter sp., LD12 and LD28 clusters and bacteria affiliated with subcluster I of Methylophilus, were found to dominate in bacterioplankton communities at higher temperatures (25 and 35 °C), regardless of nutrient conditions. We also observed that the rate of BCC change increased at higher temperatures and this increase was more pronounced in nutrient-enriched microcosms. These results indicated that bacterioplankton communities become unstable and decrease in size with increased temperature and in nutrient-enriched conditions.

Synthesis of knowledge on marine biodiversity in European Seas: from census to sustainable management

The recently completed European Census of Marine Life, conducted within the framework of the global Census of Marine Life programme (2000–2010), markedly enhanced our understanding of marine biodiversity in European Seas, its importance within ecological systems, and the implications for human use. Here we undertake a synthesis of present knowledge of biodiversity in European Seas and identify remaining challenges that prevent sustainable management of marine biodiversity in one of the most exploited continents of the globe. Our analysis demonstrates that changes in faunal standing stock with depth depends on the size of the fauna, with macrofaunal abundance only declining with increasing water depth below 1000 m, whilst there was no obvious decrease in meiofauna with increasing depth. Species richness was highly variable for both deep water macro- and meio- fauna along latitudinal and longitudinal gradients. Nematode biodiversity decreased from the Atlantic into the Mediterranean whilst latitudinal related biodiversity patterns were similar for both faunal groups investigated, suggesting that the same environmental drivers were influencing the fauna. While climate change and habitat degradation are the most frequently implicated stressors affecting biodiversity throughout European Seas, quantitative understanding, both at individual and cumulative/synergistic level, of their influences are often lacking. Full identification and quantification of species, in even a single marine habitat, remains a distant goal, as we lack integrated data-sets to quantify these. While the importance of safeguarding marine biodiversity is recognised by policy makers, the lack of advanced understanding of species diversity and of a full survey of any single habitat raises huge challenges in quantifying change, and facilitating/prioritising habitat/ecosystem protection. Our study highlights a pressing requirement for more complete biodiversity surveys to be undertaken within contrasting habitats, together with investigations in biodiversity-ecosystem functioning links and identification of separate and synergistic/cumulative human-induced impacts on biodiversity.

Beyond the genome: community-level analysis of the microbial world

The development of culture-independent strategies to study microbial diversity and function has led to a revolution in microbial ecology, enabling us to address fundamental questions about the distribution of microbes and their influence on Earth's biogeochemical cycles. This article discusses some of the progress that scientists have made with the use of so-called "omic" techniques (metagenomics, metatranscriptomics, and metaproteomics) and the limitations and major challenges these approaches are currently facing. These 'omic methods have been used to describe the taxonomic structure of microbial communities in different environments and to discover new genes and enzymes of industrial and medical interest. However, microbial community structure varies in different spatial and temporal scales and none of the 'omic techniques are individually able to elucidate the complex aspects of microbial communities and ecosystems. In this article we highlight the importance of a spatiotemporal sampling design, together with a multilevel 'omic approach and a community analysis strategy (association networks and modeling) to examine and predict interacting microbial communities and their impact on the environment.

The biogeography of fungal communities in wetland sediments along the Changjiang River and other sites in China

Whether fungal community structure depends more on historical factors or on contemporary factors is controversial. This study used culture-dependent and -independent (polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)) methods to assess the influence of historical and contemporary factors on the distributions of fungi in the wetland sediments at 10 locations along the Changjiang River and at 10 other locations in China. The culture-dependent approach detected greater species diversity (177 operational taxonomic units (OTUs)) than PCR-DGGE analysis (145 OTUs), and the species in the genera of Penicillium (relative frequency=16.8%), Fusarium (15.4%), Aspergillus (7.6%), Trichoderma (5.8%) and Talaromyces (4.2%) were dominant. On the basis of DGGE data, fungal diversity along the Changjiang River increased from upstream to downstream; altitude explained 44.8% of this variation in diversity. And based on the data from all 20 locations, the fungal communities were geographically clustered into three groups: Southern China, Northern China and the Qinghai-Tibetan Plateau. Multivariate regression tree analysis for data from the 20 locations indicated that the fungal community was influenced primarily by location (which explained 61.8% of the variation at a large scale), followed by total potassium (9.4%) and total nitrogen (3.5%) at a local scale. These results are consistent with the concept that geographic distance is the dominant factor driving variation in fungal diversity at a regional scale (1000-4000 km), whereas environmental factors (total potassium and total nitrogen) explain variation in fungal diversity at a local scale (<1000 km).

Marine bacteria exhibit a bipolar distribution

The microbial cosmopolitan dispersion hypothesis often invoked to explain distribution patterns driven by high connectivity of oceanographic water masses and widespread dispersal ability has never been rigorously tested. By using a global marine bacterial dataset and iterative matrix randomization simulation, we show that marine bacteria exhibit a significantly greater dispersal limitation than predicted by our null model using the "everything is everywhere" tenet with no dispersal limitation scenario. Specifically, marine bacteria displayed bipolar distributions (i.e., species occurring exclusively at both poles and nowhere else) significantly less often than in the null model. Furthermore, we observed fewer taxa present in both hemispheres but more taxa present only in a single hemisphere than expected under the null model. Each of these trends diverged further from the null expectation as the compared habitats became more geographically distant but more environmentally similar. Our meta-analysis supported a latitudinal gradient in bacterial diversity with higher richness at lower latitudes, but decreased richness toward the poles. Bacteria in the tropics also demonstrated narrower latitudinal ranges at lower latitudes and relatively larger ranges in higher latitudes, conforming to the controversial macroecological pattern of the "Rapoport rule." Collectively, our findings suggest that bacteria follow biogeographic patterns more typical of macroscopic organisms, and that dispersal limitation, not just environmental selection, likely plays an important role. Distributions of microbes that deliver critical ecosystem services, particularly those in polar regions, may be vulnerable to the same impacts that environmental stressors, climate warming, and degradation in habitat quality are having on biodiversity in animal and plant species.

A global perspective on marine photosynthetic picoeukaryote community structure

A central goal in ecology is to understand the factors affecting the temporal dynamics and spatial distribution of microorganisms and the underlying processes causing differences in community structure and composition. However, little is known in this respect for photosynthetic picoeukaryotes (PPEs), algae that are now recognised as major players in marine CO2 fixation. Here, we analysed dot blot hybridisation and cloning-sequencing data, using the plastid-encoded 16S rRNA gene, from seven research cruises that encompassed all four ocean biomes. We provide insights into global abundance, α- and β-diversity distribution and the environmental factors shaping PPE community structure and composition. At the class level, the most commonly encountered PPEs were Prymnesiophyceae and Chrysophyceae. These taxa displayed complementary distribution patterns, with peak abundances of Prymnesiophyceae and Chrysophyceae in waters of high (25:1) or low (12:1) nitrogen:phosphorus (N:P) ratio, respectively. Significant differences in phylogenetic composition of PPEs were demonstrated for higher taxonomic levels between ocean basins, using Unifrac analyses of clone library sequence data. Differences in composition were generally greater between basins (interbasins) than within a basin (intrabasin). These differences were primarily linked to taxonomic variation in the composition of Prymnesiophyceae and Prasinophyceae whereas Chrysophyceae were phylogenetically similar in all libraries. These data provide better knowledge of PPE community structure across the world ocean and are crucial in assessing their evolution and contribution to CO2 fixation, especially in the context of global climate change.

Biogeography of bacterioplankton in the tropical seawaters of Singapore

Knowledge about the biogeography of marine bacterioplankton on the global scale in general and in Southeast Asia in particular has been scarce. This study investigated the biogeography of bacterioplankton community in Singapore seawaters. Twelve stations around Singapore island were sampled on different schedules over 1 year. Using PCR-DNA fingerprinting, DNA cloning and sequencing, and microarray hybridization of the 16S rRNA genes, we observed clear spatial variations of bacterioplankton diversity within the small area of the Singapore seas. Water samples collected from the Singapore Strait (south) throughout the year were dominated by DNA sequences affiliated with Cyanobacteria and Alphaproteobacteria that were believed to be associated with the influx of water from the open seas in Southeast Asia. On the contrary, water in the relatively polluted Johor Strait (north) were dominated by Betaproteobacteria, Gammaproteobacteria, and Bacteroidetes and that were presumably associated with river discharge and the relatively eutrophic conditions of the waterway. Bacterioplankton diversity was temporally stable, except for the episodic surge of Pseudoalteromonas, associated with algal blooms. Overall, these results provide valuable insights into the diversity of bacterioplankton communities in Singapore seas and the possible influences of hydrological conditions and anthropogenic activities on the dynamics of the communities.

Contrasting extracellular enzyme activities of particle-associated bacteria from distinct provinces of the North Atlantic Ocean

Microbial communities play a key role in the marine carbon cycle, processing much of phytoplankton-derived organic matter. The composition of these communities varies by depth, season, and location in the ocean; the functional consequences of these compositional variations for the carbon cycle are only beginning to be explored. We measured the abilities of microbial communities in the large-particle fraction (retained by a 10-μm pore-size cartridge filter) to enzymatically hydrolyze high molecular weight substrates, and therefore initiate carbon remineralization in four distinct oceanic provinces: the boreal polar (BPLR), the Arctic oceanic (ARCT), the North Atlantic drift (NADR), and the North Atlantic subtropical (NAST) provinces. Since we expected the large-particle fraction to include phytoplankton cells, we measured the hydrolysis of polysaccharide substrates (laminarin, fucoidan, xylan, and chondroitin sulfate) expected to be associated with phytoplankton. Hydrolysis rates and patterns clustered into two groups, the BPLR/ARCT and the NADR/NAST. All four substrates were hydrolyzed by the BPLR/ARCT communities; hydrolysis rates of individual substrate varied by factors of ca. 1–4. In contrast, chondroitin was not hydrolyzed in the NADR/NAST, and hydrolytic activity was dominated by laminarinase. Fluorescence in situ hybridization of the large-particle fraction post-incubation showed a substantial contribution (15–26%) of CF319a-positive cells (Bacteroidetes) to total DAPI-stainable cells. Concurrent studies of microbial community composition and of fosmids from these same stations also demonstrated similarities between BPLR and ARCT stations, which were distinct from the NADR/NAST stations. Together, these data support a picture of compositionally as well as functionally distinct communities across these oceanic provinces.

Temperature dependence of evolutionary diversification: differences between two contrasting model taxa support the metabolic theory of ecology

Biodiversity patterns are largely determined by variation of diversification rates across clades and geographic regions. Although there are multiple reasons for this variation, it has been hypothesized that metabolic rate is the crucial driver of diversification of evolutionary lineages. According to the metabolic theory of ecology (MTE), metabolic rate - and consequently speciation - is driven mainly by body size and environmental temperature. As environmental temperature affects metabolic rate in ecto- and endotherms differently, its impact on diversification rate should also differ between the two types of organisms. Employing two independent approaches, we analysed correlates of speciation rates and, ultimately, net diversification rates for two contrasting taxa: plethodontid salamanders and carnivoran mammals. Whereas in the ectothermic plethodontids speciation rates positively correlated with environmental temperature, in the endothermic carnivorans a reverse, negative correlation was detected. These findings comply with predictions of the MTE and suggest that similar geographic patterns of biodiversity across taxa (e.g. ecto- and endotherms) might have been generated by different ecological and evolutionary processes.

Ectobiotic and endobiotic bacteria associated with Eutreptiella sp. isolated from Long Island Sound

Diversity and functional association of bacteria with Eutreptiella sp. was investigated. 16S rDNA analysis of ectobiotic bacteria revealed various lineages of Alphaproteobacteria and abundant Gammaproteobacteria, specifically Marinobacter. Antibiotic treatment yielded axenic cultures, and experiments based on them indicated that ectobiotic bacteria likely provide vitamin B(12) and other growth-enhancing factors for the alga. Further, DAPI staining and transmission electron microscopy revealed endobiotic bacteria in the cytoplasm of algal cells. 16S rDNA analysis showed that the bacteria belonged to one species that was most closely related to Rickettsiales endosymbionts of other organisms and phylogenetically affiliated with a new group of aquatic Rickettsiales. Observations from a diel experiment indicated that the endobiotic bacteria reproduced asynchronously with Eutreptiella sp. and had no adverse effects on lipid production (bioenergetics) or growth of the host alga. Our study reveals a diverse microbiome associated with this euglenoid alga, offering a system for studying the roles of algae-bacteria associations.

A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA

With an unprecedented decade-long time series from a temperate eutrophic lake, we analyzed bacterial and environmental co-occurrence networks to gain insight into seasonal dynamics at the community level. We found that (1) bacterial co-occurrence networks were non-random, (2) season explained the network complexity and (3) co-occurrence network complexity was negatively correlated with the underlying community diversity across different seasons. Network complexity was not related to the variance of associated environmental factors. Temperature and productivity may drive changes in diversity across seasons in temperate aquatic systems, much as they control diversity across latitude. While the implications of bacterioplankton network structure on ecosystem function are still largely unknown, network analysis, in conjunction with traditional multivariate techniques, continues to increase our understanding of bacterioplankton temporal dynamics.

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.