Comparison between two methods of assaying relative microbial activity in marine environments.

Two methods for determining relative microbial activity in the marine environment were compared. In one method, a single concentration of a labeled substrate was used to calculate rates of substrate utilization; in the other, multiple concentrations of the same substrate (heterotrophic activity method) were used to calculate maximum potential substrate utilization rates. These studies were made on 232 seawater and 79 sediment samples taken from a variety of marine environments. The highest correlations between these two methods were seen in the sediment samples tested. The lowest correlation coerfficient seen in the sediment samples was 0.90, and the highest was 0.98. In seawater samples (six studies), the lowest correlation coefficient was 0.77 and the highest was 0.95. The correlation between these two methods was also substrate concentration dependent. Higher correlation coefficients were observed when higher substrate concentrations were used. Under certain conditions, these two methods appear to be comparable for estimating relative levels of microbial activity in the marine environment.     

Activity and growth of microbial populations in pressurized deep-sea sediment and animal gut samples

Benthic animals and sediment samples were collected at deep-sea stations in the northwest (3,600-m depth) and southeast (4,300- and 5200-m depths) Atlantic Ocean. Utilization rates of [14C]glutamate (0.67 to 0.74 nmol) in sediment suspensions incubated at in situ temperatures and pressures (3 to 5 degrees C and 360, 430, or 520 atmospheres) were relatively slow, ranging from 0.09 to 0.39 nmol g-1 day-1, whereas rates for pressurized samples of gut suspensions varied widely, ranging from no detectable activity to a rapid rate of 986 nmol g-1 day-1. Gut flora from a holothurian specimen and a fish demonstrated rapid, barophilic substrate utilization, based on relative rates calculated for pressurized samples and samples held at 1 atm (101.325 kPa). Substrate utilization by microbial populations in several sediment samples was not inhibited by in situ pressure. Deep-sea pressures did not restrict growth, measured as doubling time, of culturable bacteria present in a northwest Atlantic sediment sample and in a gut suspension prepared from an abyssal scavenging amphipod. From the results of this study, it was concluded that microbial populations in benthic environments can demonstrate significant metabolic activity under deep-ocean conditions of temperature and pressure. Furthermore, rates of microbial activity in the guts of benthic macrofauna are potentially more rapid than in surrounding deep-sea sediments.     

Activity and growth of microbial populations in pressurized deep-sea sediment and animal gut samples.

Benthic animals and sediment samples were collected at deep-sea stations in the northwest (3,600-m depth) and southeast (4,300- and 5200-m depths) Atlantic Ocean. Utilization rates of [14C]glutamate (0.67 to 0.74 nmol) in sediment suspensions incubated at in situ temperatures and pressures (3 to 5 degrees C and 360, 430, or 520 atmospheres) were relatively slow, ranging from 0.09 to 0.39 nmol g-1 day-1, whereas rates for pressurized samples of gut suspensions varied widely, ranging from no detectable activity to a rapid rate of 986 nmol g-1 day-1. Gut flora from a holothurian specimen and a fish demonstrated rapid, barophilic substrate utilization, based on relative rates calculated for pressurized samples and samples held at 1 atm (101.325 kPa). Substrate utilization by microbial populations in several sediment samples was not inhibited by in situ pressure. Deep-sea pressures did not restrict growth, measured as doubling time, of culturable bacteria present in a northwest Atlantic sediment sample and in a gut suspension prepared from an abyssal scavenging amphipod. From the results of this study, it was concluded that microbial populations in benthic environments can demonstrate significant metabolic activity under deep-ocean conditions of temperature and pressure. Furthermore, rates of microbial activity in the guts of benthic macrofauna are potentially more rapid than in surrounding deep-sea sediments.     

褐菖鲉肝CYP 1A作为生物标志物监测厦门海域石油污染状况

以褐菖鲉为实验鱼类,以鱼肝微粒体CYP1A 生物标志物(EROD活性和CYP1A蛋白表达量)为指标,在厦门海域开展了两次野外监测实验,研究EROD活性和CYP1A蛋白表达量的变化,以及它们与海水和沉积物中石油类和重金属含量之间的相关性。结果表明,在现场属于一类海水的石油类浓度(0.0121-0.0242 mg/L)条件下,石油类就能够显著诱导褐菖鲉肝EROD活性和CYP1A蛋白表达量,鱼肝EROD活性和CYP1A蛋白表达量与海水中石油类含量均呈现极显著正相关,CYP1A蛋白表达量比EROD活性较为敏感和稳定。此外,在监测实验中,尚未发现这两种生物标志物受所监测海区的海水和沉积物重金属含量的影响。因此,利用褐菖鲉肝微粒体EROD活性和CYP1A蛋白表达量作为生物标志物监测海洋石油类及其PAHs污染是可行的,在海洋环境石油类污染监测及其生化效应评价中具有重要的应用价值。而且,把这两种生物标志物结合起来加以研究并推广应用将更有意义。     

UniFrac: a new phylogenetic method for comparing microbial communities

We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. Our results reveal that (i) cultured isolates from ice, water, and sediment resemble each other and environmental clone sequences from sea ice, but not environmental clone sequences from sediment and water; (ii) the geographical location does not correlate strongly with bacterial community differences in ice and sediment from the Arctic and Antarctic; and (iii) bacterial communities differ between terrestrially impacted seawater (whether polar or temperate) and warm oligotrophic seawater, whereas those in individual seawater samples are not more similar to each other than to those in sediment or ice samples. These results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.     

Polycyclic aromatic hydrocarbons and heavy metals in Kostrena coastal area

The aim of this study was to determine pollution by polycyclic aromatic hydrocarbons (PAH) and heavy metals in seawater and sediment in Kostrena coastal area, as well as their toxicity using bioluminescence based tests. Total PAH concentration in seawater ranged 1.7-155.3 ng/L. The share of carcinogenetic PAH was relatively high, ranging 22-48.3%. Nickel concentrations in seawater were beyond detection limits (< 0.1 microg/L), vanadium concentrations ranged 0.66-1.96 microg/L, chrome concentrations were beyond detection limits, and copper concentrations were also beyond detection limits or extremely low (up to 0.32 microg/L). EC50 values in seawater ranged 23.80-90.90 ng/L. Correlation between total PAH concentration and toxicity of seawater showed strong connection between them (r = 0.9579). Total PAH concentration in marine sediment ranged 58.02-1116 microg/kg dry weight (d.w.). The share of carcinogenetic PAH was extremely high ranging 10-53%. Nickel concentrations in marine sediment ranged 8-24 mg/kg d.w., vanadium concentrations ranged 24-42 mg/kg d.w., chrome concentrations ranged 11-19 mg/kg d.w., and copper concentrations ranged 7-25 mg/kg d.w. EC50 values in marine sediment ranged 818-4596 microg/kg d.w. Correlation between total PAH concentration and toxicity of marine sediment showed weak connection between them (r = 0.2590). Previous studies of seawater samples from areas of the Adriatic sea under the direct influence of oil industry did not include concentrations of heavy metals, which makes our study the first to present such comprehensive results. Our results point out the need for further evaluations and following of marine environment pollution and its consequences on living organisms and marine ecosystem in whole.     

Microbial community composition and function in permanently cold seawater and sediments from an arctic fjord of svalbard

Heterotrophic microbial communities in seawater and sediments metabolize much of the organic carbon produced in the ocean. Although carbon cycling and preservation depend critically on the capabilities of these microbial communities, their compositions and capabilities have seldom been examined simultaneously at the same site. To compare the abilities of seawater and sedimentary microbial communities to initiate organic matter degradation, we measured the extracellular enzymatic hydrolysis rates of 10 substrates (polysaccharides and algal extracts) in surface seawater and bottom water as well as in surface and anoxic sediments of an Arctic fjord. Patterns of enzyme activities differed between seawater and sediments, not just quantitatively, in accordance with higher cell numbers in sediments, but also in their more diversified enzyme spectrum. Sedimentary microbial communities hydrolyzed all of the fluorescently labeled polysaccharide and algal extracts, in most cases at higher rates in subsurface than surface sediments. In seawater, in contrast, only 5 of the 7 polysaccharides and 2 of the 3 algal extracts were hydrolyzed, and hydrolysis rates in surface and deepwater were virtually identical. To compare bacterial communities, 16S rRNA gene clone libraries were constructed from the same seawater and sediment samples; they diverged strongly in composition. Thus, the broader enzymatic capabilities of the sedimentary microbial communities may result from the compositional differences between seawater and sedimentary microbial communities, rather than from gene expression differences among compositionally similar communities. The greater number of phylum- and subphylum-level lineages and operational taxonomic units in sediments than in seawater samples may reflect the necessity of a wider range of enzymatic capabilities and strategies to access organic matter that has already been degraded during passage through the water column. When transformations of marine organic matter are considered, differences in community composition and their different abilities to access organic matter should be taken into account.     

Field Observations of Methane Concentrations and Oxidation Rates in the Southeastern Bering Sea

Measurements of methane oxidation rates were made in southeastern Bering Sea water samples with [¹⁴C]methane. The rate at which ¹⁴CO₂ evolved from samples exposed to one methane concentration was defined as the relative methane oxidation rate. Rate determinations at three methane concentrations were used to estimate methane oxidation kinetics. The rate constant calculated from the kinetics and the observed methane concentration in the same water sample were used to calculate an in situ methane oxidation rate and the turnover time. First-order kinetics were observed in essentially all experiments in which methane oxidation kinetics were measured. Relative methane oxidation rates were greater in waters collected at inshore stations than at the offshore stations and were greater in bottom samples than in surface samples. In most water samples analyzed, there was essentially no radioactivity associated with the cells. The resulting respiration percentages were therefore very high with a mean of >98%. These data suggest that most of the methane was used by the microflora as an energy source and that very little of it was used in biosynthesis. The relative methane oxidation rates were not closely correlated with methane concentrations and did not appear to be linked to either oxygen or dissolved inorganic nitrogen concentrations. However, there was a significant correlation with relative microbial activity. Our data suggest that the methane oxidizers were associated with the general microbial heterotrophic community. Since these organisms did not appear to be using methane as a carbon source, it is unlikely that they have been isolated and identified as methane oxidizers in the past.     

Influence of Deep Ocean Sewage Outfalls on the Microbial Activity of the Surrounding Sediment

The microbial activity near two deep ocean sewage outfalls off the coast of the island of Oahu, Hawaii, was characterized. Water samples and sediment samples to a depth of 4.5 cm were analyzed from an area of approximately 4.5 × 10⁴ m² surrounding the outfalls. Although the effluent water at both sites exhibited heterotrophic activity that was 2 orders of magnitude greater than water from a control site, ambient water samples taken within 1 m of the discharge ports exhibited activity only twice that of the control water. The heterotrophic activity of the outfall sediment was only elevated above that of the control site for surface samples collected within 10 m of the outfall. Likewise, the rates of microbial nucleic acid synthesis and carbon production in the sediment were only elevated immediately adjacent to the outfalls. Total microbial biomass, as determined by the ATP content of the sediment, varied spatially but was generally elevated at the outfall sites. The specific growth rates calculated for the sediment microbial populations, however, were not greater at the outfall sites. At one site the rocks surrounding the diffuser pipe were covered with copious amounts of slime that appeared to be composed entirely of microbial cells and filaments. This microbial mat was extremely active with respect to heterotrophic activity and biomass production. Overall, it appears that the impact of the sewage discharge on the ambient seawater microbiota is slight and that the effect on the sediment microbiota is confined to an area immediately adjacent to the diffuser ports. In the sand itself, the effect is limited to the upper 2 cm at most.     

The role of sinking particles in the overwintering process of Vibrio parahaemolyticus in a marine environment

Abstract The behavioral pattern of Vibrio parahaemolytics during the winter season (December 1988 to March 1989) in the water column, sediment, plankton and sinking particles was determined in a eutrophic marine environment. A total of 15 environmental parameters and seven microbial characteristics were examined. This halophile was isolated sporadically from bottom water and plankton materials, whereas it was undetectable in the surface water and sediment samples. However, V. parahaemolyticus was isolated from the sinking particles continuously throughout the sampling period with highest counts during February 1989. Out of 195 strains identified, 10 Vibrio spp. and 3 Listonella spp. were observed of which V. alginolyticus was predominantly isolated irrespective of the samples tested. Simple correlation and multiple regression analyses show that the occurrence of V. parahaemolyticus is not governed by any single biotic or abiotic factor of the environment. Possibly, the cumulative effect of all these environmental parameters on the distribution of V. parahaemolyticus is conceivable.     

Enzyme inhibitors and other bioactive compounds from marine actinomycetes

Several enzyme-inhibitor-producing actinomycetes were isolated from various samples collected from the marine environment and characterized. Most of them produced novel compounds that are useful in medicine and agriculture. Actinomycete strain no. 18, which produces antibiotics against Gram-positive bacteria only in the presence of seawater, was isolated from sediment sampled from neritic sea water and characterized. The production of antibiotics was observed at seawater concentrations ranging from 60 to 110% (v/v). Thus, the production was seawater-dependent. The production of tetrodotoxin (TTX), known otherwise as puffer fish toxin, was investigated in various actinomycetes collected from the marine environment. Of 10 isolates from various sea areas, 9 produced TTX as judged by their retention times on high-performance liquid chromatography (HPLC). To our knowledge, this is the first report of actinomycetes from the marine environment that produce TTX.     

Bioturbation: impact on the marine nitrogen cycle

Sediments play a key role in the marine nitrogen cycle and can act either as a source or a sink of biologically available (fixed) nitrogen. This cycling is driven by a number of microbial remineralization reactions, many of which occur across the oxic/anoxic interface near the sediment surface. The presence and activity of large burrowing macrofauna (bioturbators) in the sediment can significantly affect these microbial processes by altering the physicochemical properties of the sediment. For example, the building and irrigation of burrows by bioturbators introduces fresh oxygenated water into deeper sediment layers and allows the exchange of solutes between the sediment and water column. Burrows can effectively extend the oxic/anoxic interface into deeper sediment layers, thus providing a unique environment for nitrogen-cycling microbial communities. Recent studies have shown that the abundance and diversity of micro-organisms can be far greater in burrow wall sediment than in the surrounding surface or subsurface sediment; meanwhile, bioturbated sediment supports higher rates of coupled nitrification-denitrification reactions and increased fluxes of ammonium to the water column. In the present paper we discuss the potential for bioturbation to significantly affect marine nitrogen cycling, as well as the molecular techniques used to study microbial nitrogen cycling communities and directions for future study.     

Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediments

The prokaryote community activity and structural characteristics within marine sediment sampled across a continental shelf area located off eastern Antarctica (66 degrees S, 143 degrees E; depth range, 709 to 964 m) were studied. Correlations were found between microbial biomass and aminopeptidase and chitinase rates, which were used as proxies for microbial activity. Biomass and activity were maximal within the 0- to 3-cm depth range and declined rapidly with sediment depths below 5 cm. Most-probable-number counting using a dilute carbohydrate-containing medium recovered 1.7 to 3.8% of the sediment total bacterial count, with mostly facultatively anaerobic psychrophiles cultured. The median optimal growth temperature for the sediment isolates was 15 degrees C. Many of the isolates identified belonged to genera characteristic of deep-sea habitats, although most appear to be novel species. Phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether analyses indicated that the samples contained lipid components typical of marine sediments, with profiles varying little between samples at the same depth; however, significant differences in PLFA profiles were found between depths of 0 to 1 cm and 13 to 15 cm, reflecting the presence of a different microbial community. Denaturing gradient gel electrophoresis (DGGE) analysis of amplified bacterial 16S rRNA genes revealed that between samples and across sediment core depths of 1 to 4 cm, the community structure appeared homogenous; however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. Sequencing of DGGE bands and rRNA probe hybridization analysis revealed that the major community members belonged to delta proteobacteria, putative sulfide oxidizers of the gamma proteobacteria, Flavobacteria, Planctomycetales, and Archaea. rRNA hybridization analyses also indicated that these groups were present at similar levels in the top layer across the shelf region.     

Mechanisms for Soil Moisture Effects on Activity of Nitrifying Bacteria

Moisture may limit microbial activity in a wide range of environments including salt water, food, wood, biofilms, and soils. Low water availability can inhibit microbial activity by lowering intracellular water potential and thus reducing hydration and activity of enzymes. In solid matrices, low water content may also reduce microbial activity by restricting substrate supply. As pores within solid matrices drain and water films coating surfaces become thinner, diffusion path lengths become more tortuous, and the rate of substrate diffusion to microbial cells declines. We used two independent techniques to evaluate the relative importance of cytoplasmic dehydration versus diffusional limitations in controlling rates of nitrification in soil. Nitrification rates in shaken soil slurries, in which NH(inf4)(sup+) was maintained at high concentrations and osmotic potential was controlled by the addition of K(inf2)SO(inf4), were compared with rates in moist soil incubations, in which substrate supply was controlled by the addition of NH(inf3) gas. Comparison of results from these techniques demonstrated that diffusional limitation of substrate supply and adverse physiologic effects associated with cell dehydration can explain all of the decline in activity of nitrifying bacteria at low soil water content. However, the relative importance of substrate limitation and dehydration changes at different water potentials. For the soil-microbial system we worked with, substrate limitation was the major inhibiting factor when soil water potentials were greater than -0.6 MPa, whereas adverse physiological effects associated with cell dehydration were more inhibiting at water potentials of less than -0.6 MPa.     

UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. Our results reveal that (i) cultured isolates from ice, water, and sediment resemble each other and environmental clone sequences from sea ice, but not environmental clone sequences from sediment and water; (ii) the geographical location does not correlate strongly with bacterial community differences in ice and sediment from the Arctic and Antarctic; and (iii) bacterial communities differ between terrestrially impacted seawater (whether polar or temperate) and warm oligotrophic seawater, whereas those in individual seawater samples are not more similar to each other than to those in sediment or ice samples. These results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.     

Evidence for an enhanced substrate requirement by marine mesophilic bacterial isolates at minimal growth temperatures

Bacterial isolates from the subtropical southeastern continental shelf were cultured in a matrix of temperature and substrate concentrations encompassing a range of temperature and substrate concentrations equal to and exceeding natural ones. At the annual minimum temperature, marine heterotrophic bacterial isolates required higher concentrations of dissolved substrates for active growth than are usually found in seawater. We show this to result from a nonlinear interaction of the combined effects of temperature and substrate concentration on bacterial growth and respiratory rate. As a result, bacterial and protozoan utilization of phytoplankton production during winter and early spring is low, permitting greater energy flow to zooplankton and benthic animals, while in late spring, summer, and fall, the microbial loop dominates energy flux and organic carbon utilization. Escherichia coli shows a similar nonlinear response to temperature at minimal substrate concentrations, albeit at a higher range of concentrations than were utilized by the marine isolates. Thus, bacteria from subtropical regions are shown to have a differential growth response near the minimum temperature for growth, depending on the concentration of available substrates. Offprint requests to: W.J. Wiebe.     

马里亚纳海沟共培养细菌多样性动态变化及潜在微生物互作关系

马里亚纳海沟是世界已知最深的海沟,其寡营养、高压、低温、低氧等极端的深海环境孕育出独特的细菌群落结构及多样性特征。选取寡营养培养基对马里亚纳海沟海水及表层沉积物分别进行液体共培养,并在不同培养阶段取样进行高通量测序,分析细菌群落结构组成及其多样性的动态变化,探讨微生物之间可能的互作关系。研究结果表明：液体共培养样品中一共检测到19个门、34个纲、76个目、131个科、227个属的细菌,其中变形菌门（Proteobacteria）和拟杆菌门（Bacteroidetes）为优势菌群,其次为厚壁菌门（Firmicutes）;与其他样品相比,1000米海水样品中细菌群落的多样性最高,并且蓝细菌门（Cyanobacteria）具有更高的相对丰度。共培养样品中细菌丰富度、多样性、群落结构均随培养时间而改变,其中共培养中期样品的细菌多样性较高;表层沉积物样本中,盐单胞菌属（Halomonas）可能由于较强的竞争能力在共培养后期占据优势地位。基因功能预测与代谢通路富集结果显示,随着共培养时间的增加,微生物生长相关的代谢通路丰度明显下降,而与互作相关的代谢通路丰度明显增加。共培养样品检测到的细菌多样性远高于单独分离培养的多样性,仅有少量菌属为单独分离培养与共培养样品均检测到的共有属。综上所述,马里亚纳海沟细菌群落中存在竞争、互利共生的相互作用,共培养法有利于揭示细菌间的互作关系。研究为深渊及深海等极端环境下微生物生态系统组成及维持奠定了理论基础,也为进一步研究极端微生物的生存策略提供了科学指导。     

Dissolved organic phosphorus utilization by the marine bacterium Ruegeria pomeroyi DSS-3 reveals chain length-dependent polyphosphate degradation

Dissolved organic phosphorus (DOP) is a critical nutritional resource for marine microbial communities. However, the relative bioavailability of different types of DOP, such as phosphomonoesters (P-O-C) and phosphoanhydrides (P-O-P), is poorly understood. Here we assess the utilization of these P sources by a representative bacterial copiotroph, Ruegeria pomeroyi DSS-3. All DOP sources supported equivalent growth by R. pomeroyi, and all DOP hydrolysis rates were upregulated under phosphorus depletion (−P). A long-chain polyphosphate (45polyP) showed the lowest hydrolysis rate of all DOP substrates tested, including tripolyphosphate (3polyP). Yet the upregulation of 45polyP hydrolysis under −P was greater than any other substrate analyzed. Proteomics revealed three common P acquisition enzymes potentially involved in polyphosphate utilization, including two alkaline phosphatases, PhoD and PhoX, and one 5′-nucleotidase (5′-NT). Results from DOP substrate competition experiments show that these enzymes likely have broad substrate specificities, including chain length-dependent reactivity toward polyphosphate. These results confirm that DOP, including polyP, are bioavailable nutritional P sources for R. pomeroyi, and possibly other marine heterotrophic bacteria. Furthermore, the chain-length dependent mechanisms, rates and regulation of polyP hydrolysis suggest that these processes may influence the composition of DOP and the overall recycling of nutrients within marine dissolved organic matter.     

Distribution of viral abundance in the reef environment of Key Largo, Florida.

The distribution of viral and microbial abundance in the Key Largo, Fla., reef environment was measured. Viral abundance was measured by transmission electron microscope direct counts and plaque titer on specific bacterial hosts in water and sediment samples from Florida Bay (Blackwater Sound) and along a transect from Key Largo to the outer edge of the reef tract in Key Largo Sanctuary. Water column viral direct counts were highest in Blackwater Sound of Florida Bay (1.2 x 10(7) viruses per ml), decreased to the shelf break (1.7 x 10(6) viruses per ml), and were inversely correlated with salinity (r = -0.97). Viral direct counts in sediment samples ranged from 1.35 x 10(8) to 5.3 x 10(8)/cm(3) of sediment and averaged nearly 2 orders of magnitude greater than counts in the water column. Viral direct counts (both sediment and water column measurements) exceeded plaque titers on marine bacterial hosts (Vibrio natriegens and others) by 7 to 8 orders of magnitude. Water column viral abundance did not correlate with bacterial direct counts or chlorophyll a measurements, and sediment viral parameters did not correlate with water column microbial, viral, or salinity data. Coliphage, which are indicators of fecal pollution, were detected in two water column samples and most sediment samples, yet their concentrations were relatively low (<2 to 15/liter for water column samples, and <2 to 108/cm(3) of sediment). Our findings indicate that viruses are abundant in the Key Largo environment, particularly on the Florida Bay side of Key Largo, and that processes governing their distribution in the water column (i.e., salinity and freshwater input) are independent of those governing their distribution in the sediment environment.     

Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution

There is growing concern that predicted changes to global ocean chemistry will interact with anthropogenic pollution to significantly alter marine microbial composition and function. However, knowledge of the compounding effects of climate change stressors and anthropogenic pollution is limited. Here, we used 16S and 18S rRNA (cDNA)‐based activity profiling to investigate the differential responses of selected microbial taxa to ocean acidification and oil hydrocarbon contamination under controlled laboratory conditions. Our results revealed that a lower relative abundance of sulphate‐reducing bacteria (Desulfosarcina/Desulfococcus clade) due to an adverse effect of seawater acidification and oil hydrocarbon contamination (reduced pH–oil treatment) may be coupled to changes in sediment archaeal communities. In particular, we observed a pronounced compositional shift and marked reduction in the prevalence of otherwise abundant operational taxonomic units (OTUs) belonging to the archaeal Marine Benthic Group B and Marine Hydrothermal Vent Group (MHVG) in the reduced pH–oil treatment. Conversely, the abundance of several putative hydrocarbonoclastic fungal OTUs was higher in the reduced pH–oil treatment. Sediment hydrocarbon profiling, furthermore, revealed higher concentrations of several alkanes in the reduced pH–oil treatment, corroborating the functional implications of the structural changes to microbial community composition. Collectively, our results advance the understanding of the response of a complex microbial community to the interaction between reduced pH and anthropogenic pollution. In future acidified marine environments, oil hydrocarbon contamination may alter the typical mixotrophic and k‐/r‐strategist composition of surface sediment microbiomes towards a more heterotrophic state with lower doubling rates, thereby impairing the ability of the ecosystem to recover from acute oil contamination events.