Temporal Dynamics of South End Tidal Creek (Sapelo Island, Georgia) Bacterial Communities

Bacterial community dynamics in South End tidal creek, Sapelo Island, GA, were studied over a 74-h, five-tidal-cycle period. Observations were made hourly for the first consecutive 24 hours, every 3 hours on the second day, and every 6 hours on the third day. Tide most strongly influenced bacterial community composition (high-tide versus low-tide community analysis of similarities, R = 0.41, P < 0.03). Dissolved oxygen concentration and conductivity were important proximate drivers. However, after accounting for tide and environmental variables colinear with tide, cumulative time became more important in describing community variation. In-stream physical processes, including particulate suspension and sedimentation, may explain tide-associated trends in the bacterial community composition observed.     

Chemoautotrophic Carbon Fixation Rates and Active Bacterial Communities in Intertidal Marine Sediments

Chemoautotrophy has been little studied in typical coastal marine sediments, but may be an important component of carbon recycling as intense anaerobic mineralization processes in these sediments lead to accumulation of high amounts of reduced compounds, such as sulfides and ammonium. We studied chemoautotrophy by measuring dark-fixation of ¹³C-bicarbonate into phospholipid derived fatty acid (PLFA) biomarkers at two coastal sediment sites with contrasting sulfur chemistry in the Eastern Scheldt estuary, the Netherlands. At one site where free sulfide accumulated in the pore water right to the top of the sediment, PLFA labeling was restricted to compounds typically found in sulfur and ammonium oxidizing bacteria. At the other site, with no detectable free sulfide in the pore water, a very different PLFA labeling pattern was found with high amounts of label in branched i- and a-PLFA besides the typical compounds for sulfur and ammonium oxidizing bacteria. This suggests that other types of chemoautotrophic bacteria were also active, most likely Deltaproteobacteria related to sulfate reducers. Maximum rates of chemoautotrophy were detected in first 1 to 2 centimeters of both sediments and chemosynthetic biomass production was high ranging from 3 to 36 mmol C m⁻² d⁻¹. Average dark carbon fixation to sediment oxygen uptake ratios were 0.22±0.07 mol C (mol O₂)⁻¹, which is in the range of the maximum growth yields reported for sulfur oxidizing bacteria indicating highly efficient growth. Chemoautotrophic biomass production was similar to carbon mineralization rates in the top of the free sulfide site, suggesting that chemoautotrophic bacteria could play a crucial role in the microbial food web and labeling in eukaryotic poly-unsaturated PLFA was indeed detectable. Our study shows that dark carbon fixation by chemoautotrophic bacteria is a major process in the carbon cycle of coastal sediments, and should therefore receive more attention in future studies on sediment biogeochemistry and microbial ecology.     

Enumeration and Detection of Anaerobic Ferrous Iron-Oxidizing, Nitrate-Reducing Bacteria from Diverse European Sediments

Anaerobic, nitrate-dependent microbial oxidation of ferrous iron was recently recognized as a new type of metabolism. In order to study the occurrence of three novel groups of ferrous iron-oxidizing, nitrate-reducing bacteria (represented by strains BrG1, BrG2, and BrG3), 16S rRNA-targeted oligonucleotide probes were developed. In pure-culture experiments, these probes were shown to be suitable for fluorescent in situ hybridization, as well as for hybridization analysis of denaturing gradient gel electrophoresis (DGGE) patterns. However, neither enumeration by in situ hybridization nor detection by the DGGE-hybridization approach was feasible with sediment samples. Therefore, the DGGE-hybridization approach was combined with microbiological methods. Freshwater sediment samples from different European locations were used for enrichment cultures and most-probable-number (MPN) determinations. Bacteria with the ability to oxidize ferrous iron under nitrate-reducing conditions were detected in all of the sediment samples investigated. At least one of the previously described types of bacteria was detected in each enrichment culture. MPN studies showed that sediments contained from 1 × 10⁵ to 5 × 10⁸ ferrous iron-oxidizing, nitrate-reducing bacteria per g (dry weight) of sediment, which accounted for at most 0.8% of the nitrate-reducing bacteria growing with acetate. Type BrG1, BrG2, and BrG3 bacteria accounted for an even smaller fraction (0.2% or less) of the ferrous iron-oxidizing, nitrate-reducing community. The DGGE patterns of MPN cultures suggested that more organisms than those isolated thus far are able to oxidize ferrous iron with nitrate. A comparison showed that among the anoxygenic phototrophic bacteria, organisms that have the ability to oxidize ferrous iron also account for only a minor fraction of the population.     

The Fate of Nitrate in Intertidal Permeable Sediments

Coastal zones act as a sink for riverine and atmospheric nitrogen inputs and thereby buffer the open ocean from the effects of anthropogenic activity. Recently, microbial activity in sandy permeable sediments has been identified as a dominant source of N-loss in coastal zones, namely through denitrification. Some of the highest coastal denitrification rates measured so far occur within the intertidal permeable sediments of the eutrophied Wadden Sea. Still, denitrification alone can often account for only half of the substantial nitrate (NO₃ ⁻) consumption. Therefore, to investigate alternative NO₃ ⁻ sinks such as dissimilatory nitrate reduction to ammonium (DNRA), intracellular nitrate storage by eukaryotes and isotope equilibration effects we carried out ¹⁵NO₃ ⁻ amendment experiments. By considering all of these sinks in combination, we could quantify the fate of the ¹⁵NO₃ ⁻ added to the sediment. Denitrification was the dominant nitrate sink (50–75%), while DNRA, which recycles N to the environment accounted for 10–20% of NO₃ ⁻ consumption. Intriguingly, we also observed that between 20 and 40% of ¹⁵NO₃ ⁻ added to the incubations entered an intracellular pool of NO₃ ⁻ and was subsequently respired when nitrate became limiting. Eukaryotes were responsible for a large proportion of intracellular nitrate storage, and it could be shown through inhibition experiments that at least a third of the stored nitrate was subsequently also respired by eukaryotes. The environmental significance of the intracellular nitrate pool was confirmed by in situ measurements which revealed that intracellular storage can accumulate nitrate at concentrations six fold higher than the surrounding porewater. This intracellular pool is so far not considered when modeling N-loss from intertidal permeable sediments; however it can act as a reservoir for nitrate during low tide. Consequently, nitrate respiration supported by intracellular nitrate storage can add an additional 20% to previous nitrate reduction estimates in intertidal sediments, further increasing their contribution to N-loss.     

Denitrification in San Francisco Bay Intertidal Sediments

The acetylene block technique was employed to study denitrification in intertidal estuarine sediments. Addition of nitrate to sediment slurries stimulated denitrification. During the dry season, sediment-slurry denitrification rates displayed Michaelis-Menten kinetics, and ambient NO₃⁻ + NO₂⁻ concentrations (≤26 μM) were below the apparent K_m (50 μM) for nitrate. During the rainy season, when ambient NO₃⁻ + NO₂⁻ concentrations were higher (37 to 89 μM), an accurate estimate of the K_m could not be obtained. Endogenous denitrification activity was confined to the upper 3 cm of the sediment column. However, the addition of nitrate to deeper sediments demonstrated immediate N₂O production, and potential activity existed at all depths sampled (the deepest was 15 cm). Loss of N₂O in the presence of C₂H₂ was sometimes observed during these short-term sediment incubations. Experiments with sediment slurries and washed cell suspensions of a marine pseudomonad confirmed that this N₂O loss was caused by incomplete blockage of N₂O reductase by C₂H₂ at low nitrate concentrations. Areal estimates of denitrification (in the absence of added nitrate) ranged from 0.8 to 1.2 μmol of N₂ m⁻² h⁻¹ (for undisturbed sediments) to 17 to 280 μmol of N₂ m⁻² h⁻¹ (for shaken sediment slurries).     

Diatom-Derived Carbohydrates as Factors Affecting Bacterial Community Composition in Estuarine Sediments

Microphytobenthic biofilms in estuaries, dominated by epipelic diatoms, are sites of high primary productivity. These diatoms exude large quantities of extracellular polymeric substances (EPS) comprising polysaccharides and glycoproteins, providing a substantial pool of organic carbon available to heterotrophs within the sediment. In this study, sediment slurry microcosms were enriched with either colloidal carbohydrates or colloidal EPS (cEPS) or left unamended. Over 10 days, the fate of these carbohydrates and changes in β-glucosidase activity were monitored. Terminal restriction fragment length polymorphism (T-RFLP), DNA sequencing, and quantitative PCR (Q-PCR) analysis of 16S rRNA sequences were used to determine whether sediment bacterial communities exhibited compositional shifts in response to the different available carbon sources. Initial heterotrophic activity led to reductions in carbohydrate concentrations in all three microcosms from day 0 to day 2, with some increases in β-glucosidase activity. During this period, treatment-specific shifts in bacterial community composition were not observed. However, by days 4 and 10, the bacterial community in the cEPS-enriched sediment diverged from those in colloid-enriched and unamended sediments, with Q-PCR analysis showing elevated bacterial numbers in the cEPS-enriched sediment at day 4. Community shifts were attributed to changes in cEPS concentrations and increased β-glucosidase activity. T-RFLP and sequencing analyses suggested that this shift was not due to a total community response but rather to large increases in the relative abundance of members of the γ-proteobacteria, particularly Acinetobacter-related bacteria. These experiments suggest that taxon- and substrate-specific responses within the bacterial community are involved in the degradation of diatom-derived extracellular carbohydrates.     

Reproducing Bobcats to Cumberland Island, Georgia

Many felids are threatened by loss of habitat, lack of genetic diversity, and over-exploitation. The reintroduction of bobcats (Felis rufus) to Cumberland Island, Georgia provided an opportunity to reintroduce a mid-sized felid without the concern for species survival that is paramount with endangered species. We captured bobcats from the coastal plain region of Georgia, briefly held them in captivity, and released them on Cumberland Island. We describe and evaluate the protocols and techniques used to accomplish the reintroduction. Future reintroductions of felids should consider the problem of post-release dispersal, although our island was relatively isolated and inhibited dispersal. Also, any reintroduction effort should invest effort and resources into post-release monitoring of the population. Empirical knowledge about the effects of spatial distribution, genetics, population dynamics, especially mechanisms of population regulation, behavior, and environmental conditions on the viability of populations is critical to the conservation of endangered species. Future research of the bobcats on Cumberland Island will be able to address aspects of the population and genetic dynamics of a small, insular felid population.     

Comparison of the Levels of Bacterial Diversity in Freshwater,Intertidal Wetland,and Marine Sediments by Using Millions of Illumina Tags

Sediment, a special realm in aquatic environments, has high microbial diversity. While there are numerous reports about the microbial community in marine sediment, freshwater and intertidal sediment communities have been overlooked. The present study determined millions of Illumina reads for a comparison of bacterial communities in freshwater, intertidal wetland, and marine sediments along Pearl River, China, using a technically consistent approach. Our results show that both taxon richness and evenness were the highest in freshwater sediment, medium in intertidal sediment, and lowest in marine sediment. The high number of sequences allowed the determination of a wide variety of bacterial lineages in all sediments for reliable statistical analyses. Principal component analysis showed that the three types of communities could be well separated from phylum to operational taxonomy unit (OTU) levels, and the OTUs from abundant to rare showed satisfactory resolutions. Statistical analysis (LEfSe) demonstrated that the freshwater sediment was enriched with Acidobacteria, Nitrospira, Verrucomicrobia, Alphaproteobacteria, and Betaproteobacteria. The intertidal sediment had a unique community with diverse primary producers (such as Chloroflexi, Bacillariophyta, Gammaproteobacteria, and Epsilonproteobacteria) as well as saprophytic microbes (such as Actinomycetales, Bacteroidetes, and Firmicutes). The marine sediment had a higher abundance of Gammaproteobacteria and Deltaproteobacteria, which were mainly involved in sulfate reduction in anaerobic conditions. These results are helpful for a systematic understanding of bacterial communities in natural sediment environments.     

Influences of Infaunal Burrows on the Community Structure and Activity of Ammonia-Oxidizing Bacteria in Intertidal Sediments

Influences of infaunal burrows constructed by the polychaete (Tylorrhynchus heterochaetus) on O₂ concentrations and community structures and abundances of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in intertidal sediments were analyzed by the combined use of a 16S rRNA gene-based molecular approach and microelectrodes. The microelectrode measurements performed in an experimental system developed in an aquarium showed direct evidence of O₂ transport down to a depth of 350 mm of the sediment through a burrow. The 16S rRNA gene-cloning analysis revealed that the betaproteobacterial AOB communities in the sediment surface and the burrow walls were dominated by Nitrosomonas sp. strain Nm143-like sequences, and most of the clones in Nitrospira-like NOB clone libraries of the sediment surface and the burrow walls were related to the Nitrospira marina lineage. Furthermore, we investigated vertical distributions of AOB and NOB in the infaunal burrow walls and the bulk sediments by real-time quantitative PCR (Q-PCR) assay. The AOB and Nitrospira-like NOB-specific 16S rRNA gene copy numbers in the burrow walls were comparable with those in the sediment surfaces. These numbers in the burrow wall at a depth of 50 to 55 mm from the surface were, however, higher than those in the bulk sediment at the same depth. The microelectrode measurements showed higher NH₄⁺ consumption activity at the burrow wall than those at the surrounding sediment. This result was consistent with the results of microcosm experiments showing that the consumption rates of NH₄⁺ and total inorganic nitrogen increased with increasing infaunal density in the sediment. These results clearly demonstrated that the infaunal burrows stimulated O₂ transport into the sediment in which otherwise reducing conditions prevailed, resulting in development of high NH₄⁺ consumption capacity. Consequently, the infaunal burrow became an important site for NH₄⁺ consumption in the intertidal sediment.     

Diverse UV-B Resistance of Culturable Bacterial Community from High-Altitude Wetland Water

Isolation of most ultraviolet B (UV-B)-resistant culturable bacteria that occur in the habitat of Laguna Azul, a high-altitude wetland [4554 m above sea level (asl)] from the Northwestern Argentinean Andes, was carried out by culture-based methods. Water from this environment was exposed to UV-B radiation under laboratory conditions during 36 h, at an irradiance of 4.94 W/m². It was found that the total number of bacteria in water samples decreased; however, most of the community survived long-term irradiation (312 nm) (53.3 kJ/m²). The percentage of bacteria belonging to dominant species did not vary significantly, depending on the number of UV irradiation doses. The most resistant microbes in the culturable community were Gram-positive pigmented species (Bacillus megaterium [endospores and/or vegetative cells], Staphylococcus saprophyticus, and Nocardia sp.). Only one Gram-negative bacterium could be cultivated (Acinetobacter johnsonii). Nocardia sp. that survived doses of 3201 kJ/m² were the most resistant bacteria to UV-B treatment. This study is the first report on UV-B resistance of a microbial community isolated from high-altitude extreme environments, and proposes a method for direct isolation of UV-B-resistant bacteria from extreme irradiated environments. This article is dedicated to the memory of Carolina Colin.     

Pyrosequencing Reveals a Highly Diverse and Cultivar-Specific Bacterial Endophyte Community in Potato Roots

In this study, we examined the bacterial endophyte community of potato (Solanum tuberosum) cultivar/clones using two different molecular-based techniques (bacterial automated ribosomal intergenic spacer analysis (B-ARISA) and pyrosequencing). B-ARISA profiles revealed a significant difference in the endophytic community between cultivars (perMANOVA, p < 0.001), and canonical correspondence analysis showed a significant correlation between the community structure and plant biomass (p = 0.001). Pyrosequencing detected, on average, 477 ± 71 bacterial operational taxonomic units (OTUs, 97% genetic similarity) residing within the roots of each cultivar, with a Chao estimated total OTU richness of 1,265 ± 313. Across all cultivars, a total of 238 known genera from 15 phyla were identified. Interestingly, five of the ten most common genera (Rheinheimera, Dyadobacter, Devosia, Pedobacter, and Pseudoxanthomonas) have not, to our knowledge, been previously reported as endophytes of potato. Like the B-ARISA analysis, the endophytic communities differed between cultivar/clones (∫-libshuff, p < 0.001) and exhibited low similarities on both a presence/absence (0.145 ± 0.019) and abundance (0.420 ± 0.081) basis. Seventeen OTUs showed a strong positive (r > 0.600) or negative (r < −0.600) correlation with plant biomass, suggesting a possible link between plant production and endophyte abundance. This study represents one of the most comprehensive assessments of the bacterial endophytic communities to date, and similar analyses in other plant species, cultivars, or tissues could be utilized to further elucidate the potential contribution(s) of endophytic communities to plant physiology and production.     

Bacterial Community Composition in the Rivers of the Novaya Sibir Island

Microbiology - The results of molecular genetic studies of prokaryotic communities of river ecosystems of the central and southeastern part of the Novaya Sibir Island are presented. Five phyla...     

Bacterial Community Composition and Diversity in Methane Charged Sediments Revealed by Multitag Pyrosequencing

Bacterial diversity in sediments obtained along the Chilean margin from areas containing methane seeps, and a hydrate mound were explored by cloning and sequencing and multitag pyrosequencing (MTPS). These libraries were statistically compared to determine the robustness of taxonomic assignment derived from multiplexed pyrosequencing strategies targeting variable regions V1 and V2 of the small subunit rRNA gene for environmental studies. There was no statistical difference in the composition of the libraries, thus, MTPS was utilized to describe diversity in three geochemical zones in these environments. Unidentified Cyanobacteria isolates were abundant in the sulfate reduction zone (SRZ), Deltaproteobacteria were concentrated at the sulfate methane transition zone (SMTZ) and Chloroflexi/GNS dominated methanogenesis zone (MGZ). Although there was variation among specific groups, communities in the SRZ and MGZ did not differ significantly. However, the community dominated by Deltaproteobacteria differentiates the SMTZ from the other zones. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental file.     

Tryptophanase in Diverse Bacterial Species

The distribution of tryptophanase was studied. The highest observed specific activity, mumoles per minute per milligram (dry weight) cells, is given in parentheses after each species. Tryptophanase was inducible and repressible in Escherichia coli (.914), Paracolobactrum coliforme (.210), Proteus vulgaris (.146), Aeromonas liquefaciens (.030), Photobacterium harveyi (.035), Sphaerophorus varius (.021), Bacteroides sp. (.048), and Corynebacterium acnes (.042). The enzyme was constitutive and nonrepressible in Bacillus alvei (.013), and was inducible but not repressible by glucose in Micrococcus aerogenes (.036). Indole-positive bacteria were found in fecal or intestinal samples from a variety of animals among the mammals, reptiles, insects, molluscs, fish, crustaceans, and amphibians.     

The use of acoustics to monitor burrow-nesting white-chinned petrels Procellaria aequinoctialis at Bird Island, South Georgia

Tape recordings of two types of vocalisations were used to assess burrow occupancy by white-chinned petrels (Procellaria aequinoctialis) at South Georgia. Birds responded to the rattle call on 74% of occasions and a wheezy call on 85%, with only 10% failing to respond to both calls played one after the other. Occupancy was determined throughout the pre-egg and incubation period and results confirmed what is known about patterns of occupancy by white-chinned petrels. Adults in burrows known to hatch a chick responded on average to 69% of recordings during incubation and less than 10% in only 4% of burrows. Significant inter-site and inter-annual variations in occupancy were recorded, suggesting that this method is sensitive to changes in the number of petrels returning to breed. A sampling protocol for providing population indices for monitoring purposes is recommended. Accepted: 6 March 2000     

Annual variation in breeding biology of macaroni penguins, Eudyptes chvysolophus, at Bird Island, South Georgia

The breeding biology of the macaroni penguin, Eudyptes chrysolophus , was studied over four years, 1976 and 1986–88, at Bird Island, South Georgia. Birds were migratory, being absent during winter (May to September). Arrival at the colony was highly synchronous between years: 14–23 October, over a 7-year period. The pre-breeding, incubation and chick-brooding period was characterized by long fasts ashore, for 36 and 39 days in males and 41 days in females, alternating with long periods at sea. Within years egg-laying was highly synchronous: 95% of clutches initiated within 4–6 days. Arrival date and mean egg-laying date were later (by 3 days), and breeding population size lower (by 20%) in 1987, compared to other years. The incubation period was 35 days and comprised three long shifts, the first shared by the male and female, the second by the female and the third by the male. In 1986 and 1988 these were of 12, 12 and 9 days' duration, but in 1987 the first shift was significantly shorter: 9 days. Chicks creched at 23–25 days of age and fledged at 60 days of age. Neither chick age nor weight at creching or fledging varied between the years 1986–88. The breeding biology of macaroni penguins at Bird Island is compared with that of other Eudyptes penguins, and with the sympatric gentoo penguin, Pygoscelispupuu. There is little variation in breeding biology within the genus Eudyptes , except in the length of time spent at sea prior to the annual moult. This is much shorter at Bird Island, probably reflecting a greater food availability compared to other localities. Inter-annual variation in certain breeding parameters, e.g. laying date, breeding population size, is much greater in the gentoo penguin than in the macaroni penguin. The shorter breeding season, rearing of only one chick and proportionately lower chick fledging weight in macaroni penguins, may be linked to this species' migratory strategy.