Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated (∼5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide.

Declines in coral cover are generally associated with increases in the abundance of fleshy algae. In many cases, it remains unclear whether algae are responsible, directly or indirectly, for coral death or whether they simply settle on dead coral surfaces. Here, we show that algae can indirectly cause coral mortality by enhancing microbial activity via the release of dissolved compounds. When coral and algae were placed in chambers together but separated by a 0.02 mum filter, corals suffered 100% mortality. With the addition of the broad-spectrum antibiotic ampicillin, mortality was completely prevented. Physiological measurements showed complementary patterns of increasing coral stress with proximity to algae. Our results suggest that as human impacts increase and algae become more abundant on reefs a positive feedback loop may be created whereby compounds released by algae enhance microbial activity on live coral surfaces causing mortality of corals and further algal growth.

An unusually thick (ϳ1 cm) slime developed on a slump of finely disseminated pyrite ore within an extreme acid mine drainage site at Iron Mountain, near Redding, Calif. The slime was studied over the period of 1 year. The subaerial form of the slime distinguished it from more typical submerged streamers. Phylogenetic analysis of 16S rRNA genes revealed a diversity of sequences that were mostly novel. Nearest relatives to the majority of sequences came from iron-oxidizing acidophiles, and it appears that iron oxidation is the predominant metabolic characteristic of the organisms in the slime. The most abundant of the 16S rRNA genes detected were from organisms related to Leptospirillum species. The dominant sequence (71% of clones) may represent a new genus. Sequences within the Archaea of the Thermoplasmales lineage were detected. Most of these were only distantly related to known microorganisms. Also, sequences affiliating with Acidimicrobium were detected. Some of these were closely related to "Ferromicrobium acidophilus," and others were affiliated with a lineage only represented by environmental clones. Unexpectedly, sequences that affiliated within the delta subdivision of the Proteobacteria were detected. The predominant metabolic feature of bacteria of this subdivision is anaerobic sulfate or metal reduction. Thus, microenvironments of low redox potential possibly exist in the predominantly oxidizing environments of the slime. These results expand our knowledge of the biodiversity of acid mine drainage environments and extend our understanding of the ecology of extremely acidic systems.Dissolution of sulfide ores exposed to oxygen, water, and microorganisms results in acid production and environmentally detrimental acid mine drainage (AMD) (35). For the aqueous dissolution of sulfide ores dominated by pyrite (FeS 2 ) at low pH, ferric ion is the predominant oxidant. The overall reaction is written: FeS 2 ϩ 14Fe 3ϩ ϩ 8H 2 O315Fe 2ϩ ϩ 2SO 4 2Ϫ ϩ 16 H ϩ . The reaction is limited by the availability of ferric ion. At pH values of less than ϳ3.0, the inorganic rate of ferrous oxidation is slow, and acidophilic organisms can mediate production of ferric iron and conserve energy from this. Thus, it is not surprising that the oxidation of pyrite is greatly increased in the presence of iron-oxidizing species such as Thiobacillus ferrooxidans over the abiotic rate; see Nordstrom and Southham (36) for a discussion. Presently the understanding of biological enhanced pyrite oxidation is incomplete, but it is clear that microbial iron oxidation would replenish ferric ions for the above reaction.The best-studied organism with respect to microbial enhancement of AMD is T. ferrooxidans. Models have been proposed for its energetic characteristics (28) and role in pyrite dissolution (41), and several investigations have studied ironoxidizing and respiratory enzymes (7,11,17). However, numerous microorganisms are known for their acidiphily and iron-oxidizing capabilities, and it is apparent that different microorganisms have...

The microenvironment surrounding individual phytoplankton cells is often rich in dissolved organic matter (DOM), which can attract bacteria by chemotaxis. These "phycospheres" may be prominent sources of resource heterogeneity in the ocean, affecting the growth of bacterial populations and the fate of DOM. However, these effects remain poorly quantified due to a lack of quantitative ecological frameworks. Here, we used video microscopy to dissect with unprecedented resolution the chemotactic accumulation of marine bacteria around individual Chaetoceros affinis diatoms undergoing lysis. The observed spatiotemporal distribution of bacteria was used in a resource utilization model to map the conditions under which competition between different bacterial groups favors chemotaxis. The model predicts that chemotactic, copiotrophic populations outcompete nonmotile, oligotrophic populations during diatom blooms and bloom collapse conditions, resulting in an increase in the ratio of motile to nonmotile cells and in the succession of populations. Partitioning of DOM between the two populations is strongly dependent on the overall concentration of bacteria and the diffusivity of different DOM substances, and within each population, the growth benefit from phycospheres is experienced by only a small fraction of cells. By informing a DOM utilization model with highly resolved behavioral data, the hybrid approach used here represents a new path toward the elusive goal of predicting the consequences of microscale interactions in the ocean.bacteria-phytoplankton interactions | motility | competition | microbial loop | dissolved organic matter

Cholera disease, caused by the bacterium Vibrio cholerae, afflicts hundreds of thousands worldwide each year. Endemic to aquatic environments, V. cholerae's proliferation and dynamics in marine systems are not well understood. Here, we show that under a variety of coastal seawater conditions V. cholerae remained primarily in a free-living state as opposed to attaching to particles. Growth rates of free-living V. cholerae (micro: 0.6-2.9 day(-1)) were high (similar to reported values for the bacterial assemblages; 0.3-2.5 day(-1)) particularly in phytoplankton bloom waters. However, these populations were subject to heavy grazing-mortality by protozoan predators. Thus, grazing-mortality counterbalanced growth, keeping V. cholerae populations in check. Net population gains were observed under particularly intense bloom conditions when V. cholerae proliferated, overcoming grazing pressure terms in part via rapid growth (> 4 doublings day(-1)). Our results show V. cholerae is subject to protozoan control and capable of utilizing multiple proliferation pathways in the marine environment. These findings suggest food web effects play a significant role controlling this pathogen's proliferation in coastal waters and should be considered in predictive models of disease risk.

Feces and distal gut contents were collected from three coral reef fish species. Bacteria cell abundances, as determined via epifluorescence microscopy, ranged two orders of magnitude among the fishes. Mass-specific and apparent cell-specific hydrolytic enzyme activities in feces from Chlorurus sordidus were very high, suggesting that endogenous fish enzymes were egested into feces. Denaturing gradient gel electrophoresis profiles of 16S rRNA genes were more similar among multiple individuals of the surgeonfish Acanthurus nigricans than among individuals of the parrotfish C. sordidus or the snapper Lutjanus bohar. Analyses of feces-derived 16S rRNA gene clones revealed that at least five bacterial phyla were present in A. nigricans and that Vibrionaceae comprised 10% of the clones. Meanwhile, C. sordidus contained at least five phyla and L. bohar three, but Vibrionaceae comprised 71% and 76% of the clones, respectively. Many sequences clustered phylogenetically to cultured Vibrio spp. and Photobacterium spp. including Vibrio ponticus and Photobacterium damselae. Other Vibrionaceae-like sequences comprised a distinct phylogenetic group that may represent the presence of 'feces-specific' bacteria. The observed differences among fishes may reflect native gut microbiota and/or bacterial assemblages associated with ingested prey.

Marine bacterial and archaeal communities control global biogeochemical cycles through nutrient acquisition processes that are ultimately dictated by the metabolic requirements of individual cells. Currently lacking, however, is a sensitive, quick, and quantitative measurement of activity in these single cells. We tested the applicability of copper (I)-catalyzed cycloaddition, or "click," chemistry to observe and estimate single-cell protein synthesis activity in natural assemblages and isolates of heterotrophic marine bacteria. Incorporation rates of the non-canonical methionine bioortholog L-homopropargylglycine (HPG) were quantified within individual cells by measuring fluorescence of alkyne-conjugated Alexa Fluor®488 using epifluorescence microscopy. The method's high sensitivity, along with a conversion factor derived from two Alteromonas spp. isolates, revealed a broad range of cell-specific protein synthesis within natural microbial populations. Comparison with 35 S-methionine microautoradiography showed that a large fraction of the natural marine bacterial assemblage (15-100%), previously considered inactive by autoradiography, were actively synthesizing protein. Data pooled from 21 samples showed that cell-specific activity scaled logarithmically with cell volume. Activity distributions of each sample were fit to power-law functions, providing an illustrative and quantitative comparison of assemblages that demonstrate individual protein synthesis rates were commonly partitioned between cells in low-and high-metabolic states in our samples. The HPG method offers a simple approach to link individual cell physiology to the ecology and biogeochemistry of bacterial (micro)environments in the ocean.

Coastal milkfish (Chanos chanos) farming may be a source of organic matter enrichment for coral reefs in Bolinao, Republic of the Philippines. Interactions among microbial communities associated with the water column, corals and milkfish feces can provide insight into the ecosystem's response to enrichment. Samples were collected at sites along a transect that extended from suspended milkfish pens into the coral reef. Water was characterized by steep gradients in the concentrations of dissolved organic carbon (70-160 microM), total dissolved nitrogen (7-40 microM), chlorophyll a (0.25-10 microg l(-1)), particulate matter (106-832 microg l(-1)), bacteria (5 x 10(5)-1 x 10(6) cells ml(-1)) and viruses (1-7 x 10(7) ml(-1)) that correlated with distance from the fish cages. Particle-attached bacteria, which were observed by scanning laser confocal microscopy, increased across the gradient from < 0.1% to 5.6% of total bacteria at the fish pens. Analyses of 16S rRNA genes by denaturing gradient gel electrophoresis and environmental clone libraries revealed distinct microbial communities for each sample type. Coral libraries had the greatest number of phyla represented (range: 6-8) while fish feces contained the lowest number (3). Coral libraries also had the greatest number of 'novel' sequences (defined as < 93% similar to any sequence in the NCBI nt database; 29% compared with 3% and 5% in the feces and seawater libraries respectively). Despite the differences in microbial community composition, some 16S rRNA sequences co-occurred across sample types including Acinetobacter sp. and Ralstonia sp. Such patterns raise the question of whether bacteria might be transported from the fish pens to corals or if microenvironments at the fish pens and on the corals select for the same phylotypes. Understanding the underlying mechanisms of effluent-coral interactions will help predict the ability of coral reef ecosystems to resist and rebound from organic matter enrichment.