Sediment Microbial Populations Research Articles

Homologous recombination and gene-specific selection co-shape the vertical nucleotide diversity of mangrove sediment microbial populations.

Mangrove sediments host a diverse array of microbial populations and are characterized by high heterogeneity along their vertical depths. However, the genetic diversity within these populations is largely unknown, hindering our understanding of their adaptive evolution across the sediment depths. To elucidate their genetic diversity, we utilized metagenome sequencing to identify 16 high-frequency microbial populations comprised of two archaea and 14 bacteria from mangrove sediment cores (0-100 cm, with 10 depths) in Qi'ao Island, China. Our analysis of the genome-wide genetic variation revealed extensive nucleotide diversity in the microbial populations. The genes involved in the transport and the energy metabolism displayed a high nucleotide diversity (HND; 0.0045-0.0195; an indicator of shared minor alleles with the microbial populations). By tracking the processes of homologous recombination, we found that each microbial population was subjected to different purification selection levels at different depths (44.12% genes). This selection resulted in significant differences in synonymous/non-synonymous mutation ratio between 0-20 and 20-100 cm layers, indicating the adaptive evolutionary process of microbial populations. Furthermore, our assessment of differentiation in the allele frequencies between these two layers showed that the functional genes involved in the metabolic processes of amino acids or cofactors were highly differential in more than half of them. Together, we showed that the nucleotide diversity of microbial populations was shaped by homologous recombination and gene-specific selection, finally resulting in the stratified differentiation occurring between 0-20 and 20-100 cm. These results enhance our cognition of the microbial adaptation mechanisms to vertical environmental changes during the sedimentation process of coastal blue carbon ecosystems.

Microorganisms associated with Sporobolus anglicus, an invasive dimethylsulfoniopropionate producing salt marsh plant, are an unrecognized sink for dimethylsulfide.

BackgroundSaltmarshes are hotspots of organosulfur compound cycling due to production of dimethylsulfoniopropionate (DMSP) by benthic microorganisms, macroalgae, and saltmarsh vegetation. Degradation of DMSP is a source of dimethylsulfide (DMS), an important precursor for formation of secondary organic aerosol. Microorganisms degrading DMS play a role in controlling the amount of DMS available for emission into the atmosphere. Previous work has implicated sediment microbial populations as a major sink for DMS. Here, we show that Sporobolus anglicus (previously known as Spartina anglica), a widely distributed saltmarsh plant, is colonized by DMS-degrading microorganisms.MethodsDimethylsulfide degradation potential was assessed by gas chromatography and 13C-DMS stable isotope probing, microbial community diversity and functional genetic potential in phyllosphere and rhizosphere samples was assessed by high-throughput sequencing of 16S rRNA gene amplicons, cloning and sequencing of methanethiol oxidase genes, and by metagenomic analysis of phyllosphere microbial communities.ResultsThe DMS degradation potential of microbial communities recovered from phyllosphere and rhizosphere samples was similar. Active DMS-degraders were identified by 13C-DMS stable isotope probing and included populations related to Methylophaga and other Piscirickettsiaceae in rhizosphere samples. DMS-degraders in the phyllosphere included Xanthomonadaceae and Halothiobacillaceae. The diversity in sediment samples of the methanethiol oxidase (mtoX) gene, a marker for metabolism of methanethiol during DMS and DMSP degradation, was similar to previously detected saltmarsh mtoX, including those of Methylophaga and Methylococcaeae. Phyllosphere mtoX genes were distinct from sediment mtoX and did not include close relatives of cultivated bacteria. Microbial diversity in the phyllosphere of S. anglicus was distinct compared to those of model plants such as rice, soybean, clover and Arabidopsis and showed a dominance of Gammaproteobacteria rather than Alphaproteobacteria.ConclusionThe potential for microbial DMS degradation in the phyllosphere and rhizosphere of Sporobolus anglicus suggest that DMS cycling in saltmarshes is more complex than previously recognised and calls for a more detailed assessment of how aboveground activities affect fluxes of DMS.

Microbial populations regulate greenhouse gas emissions in Sundarban mangrove ecosystem, India

Mangrove ecosystems are significant sources of greenhouse gases (GHG) that is attributed to microbial activity. However, it is still unknown how the sediment microbial populations affect GHG emissions in mangrove ecosystem. Since little is known about microbial populations of mangroves, the present study was aimed to understand the structure and function of microbial communities in the Indian part of the Sundarban mangrove ecosystem in relation to environmental variables and variation of GHG emissions during three seasons: pre-monsoon (March–June), monsoon (July–October) and post-monsoon (November–February).Seasonal variations of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) gas samples were taken from the mangrove bed. Culture methods were used to detect twelve different types of microbes such as heterotrophic (Htp), N2 fixing (Nfix), nitrifying (Ntfn), sulfur oxidizing (Soxd), Gram-negative (GMn), Gram-positive (GMp), spore forming (Sfor), denitrifying (DNtfn), anaerobic (Anrb), phosphate solubilizing (Psol), cellulose degrading (Cdeg) bacteria and actinomycetes (Actm). In the monsoon, populations of the Htp, Anrb, Psol, and Cdeg bacteria were more prevalent, whereas populations of the GMn, GMp, Ntfn, DNtfn bacteria, and Actm bacteria were more prevalent in the post-monsoon. Monsoonal CO2 and CH4 fluxes were larger than pre-monsoon and post-monsoon, resulting in increased microbial soil respiration and breakdown of soil organic carbon. Because of higher denitrification and soil temperature, N2O flux was higher in the pre-monsoon period, followed by monsoon and post-monsoon periods. A univariate statistical correlation was employed to assess the relationships between environmental variables and different microbial populations. An ANN (artificial neural network) model was proposed to evaluate the relevance of microbial population contribution to GHG emissions, and it indicated that the Htp, Anrb, and Dntfn microbial populations were most relevant for CO2, CH4, and N2O emissions. The suggested model would be used to assess the drivers behind GHG emission in the mangroves located at different parts of the world.

Changes in freshwater sediment microbial populations during fermentation of crude glycerol

Background: This work studied how the exposure to an unusual substrate forced a change in microbial populations during anaerobic fermentation of crude glycerol, a by-product of biodiesel production, with freshwater sediment used as an inoculum. Results: The microbial associations almost completely (99.9%) utilized the glycerol contained in crude glycerol 6 g L-1 within four days, releasing gases, organic acids (acetic, butyric) and alcohols (ethanol, n-butanol) under anaerobic conditions. In comparison with control medium without glycerol, adding crude glycerol to the medium increased the amount of ethanol and n-butanol production and it was not significantly affected by incubation temperature (28°C or 37°C), nor incubation time (4 or 8 d), but it resulted in reduced amount of butyric acid. Higher volume of gas was produced at 37°C despite the fact that the overall bacterial count was smaller than the one measured at 20°C. Main microbial phyla of the inoculum were Actinobacteria, Proteobacteria and Firmicutes. During fermentation, significant changes were observed and Firmicutes, especially Clostridium spp., began to dominate, and the number of Actinobacteria and Gammaproteobacteria decreased accordingly. Concentration of Archaea decreased, especially in medium with crude glycerol. These changes were confirmed both by culturing and culture-independent (concentration of 16S rDNA) methods. Conclusions: Crude glycerol led to the adaptation of freshwater sediment microbial populations to this substrate. Changes of microbial community were a result of a community adaptation to a new source of carbon. Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:Tabla normal; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:8.0pt; mso-para-margin-left:0cm; line-height:107%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:Calibri,sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:Times New Roman; mso-bidi-theme-font:minor-bidi;}

Improving the Accuracy of Flow Cytometric Quantification of Microbial Populations in Sediments: Importance of Cell Staining Procedures.

The accuracy of flow cytometric (FCM) quantifications of microbial populations in sediments varies with FCM settings, cell extraction and staining protocols, as well as sample types. In the present study, we improve the accuracy of FCM for enumerating microorganisms inhabiting diverse lake and marine sediment types based on extensive tests with FCM settings, extraction buffer chemical compositions, cell separation methods, and staining procedures. Tests on the FCM settings, (e.g., acquisition time, rates of events) and salinity of extraction solutions show minor impacts on FCM enumerations and yields of cell extraction, respectively. Existing methods involving hydrofluoric acid (HF) treatment to release sediment-attached cells into solution prove effective on both marine and freshwater samples. Yet, different staining techniques (direct staining of cell extracts, staining of membrane-filtered cell extracts) produce clear differences in cell number estimates. We demonstrate that, while labor-intensive membrane-staining generates high cell staining efficiency and accurate cell counts that are consistent across FCM and epifluorescence microscopy-based (EFM) quantification methods, accurate cell counts determined by more time- and labor-efficient direct staining require consideration of dye concentration, sample dilution, and lithology. Yet, good agreement between the two staining methods can be achieved through sample-specific adjustments of dye concentrations and sample dilutions during direct staining. We thus present a complete protocol for FCM-based cell quantification, that includes all steps from the initial sample fixation to the final enumeration, with recommendations for buffer compositions, direct and membrane-based staining procedures, and the final FCM assay. This protocol is versatile, accurate, and reliable, as is evident from good agreement with cell quantifications by EFM and quantitative polymerase chain reaction (qPCR) of 16S rRNA genes across a wide range of sedimentary sample types.

Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches.

Hadal ocean sediments, found at sites deeper than 6,000 m water depth, are thought to contain microbial communities distinct from those at shallower depths due to high hydrostatic pressures and higher abundances of organic matter. These communities may also differ from one other as a result of geographical isolation. Here we compare microbial community composition in surficial sediments of two hadal environments—the Mariana and Kermadec trenches—to evaluate microbial biogeography at hadal depths. Sediment microbial consortia were distinct between trenches, with higher relative sequence abundances of taxa previously correlated with organic matter degradation present in the Kermadec Trench. In contrast, the Mariana Trench, and deeper sediments in both trenches, were enriched in taxa predicted to break down recalcitrant material and contained other uncharacterized lineages. At the 97% similarity level, sequence-abundant taxa were not trench-specific and were related to those found in other hadal and abyssal habitats, indicating potential connectivity between geographically isolated sediments. Despite the diversity of microorganisms identified using culture-independent techniques, most isolates obtained under in situ pressures were related to previously identified piezophiles. Members related to these same taxa also became dominant community members when native sediments were incubated under static, long-term, unamended high-pressure conditions. Our results support the hypothesis that there is connectivity between sediment microbial populations inhabiting the Mariana and Kermadec trenches while showing that both whole communities and specific microbial lineages vary between trench of collection and sediment horizon depth. This in situ biodiversity is largely missed when incubating samples within pressure vessels and highlights the need for revised protocols for high-pressure incubations.

Pharmaceutical biodegradation under three anaerobic redox conditions evaluated by chemical and toxicological analyses

Biodegradation of pharmaceutically active compounds (PhACs) in the subsurface layer of constructed wetlands (CWs) under various anaerobic redox conditions is rarely studied. In this study, CW sediment microbial populations were enriched for PhAC biodegrading organisms. Biodegradation effectivity of a mixture of six PhACs (caffeine, CAF; naproxen, NAP; metoprolol, MET; propranolol, PRO; ibuprofen, IBP; carbamazepine, CBZ) and single compounds (CAF, NAP) was investigated under nitrate reducing, sulfate reducing, and methanogenic conditions using chemical and toxicological analyses. Biodegradation efficiencies varied strongly among the six PhACs and three redox conditions chosen. CAF and NAP were completely biodegraded under sulfate reducing and methanogenic conditions whereas biodegradation efficiencies of the other PhACs were much less (MET, PRO <20%; IBP, CBZ, negligible). CAF and NAP showed significantly lower biodegradation under nitrate reducing conditions than under the other two redox conditions. No difference was found in biodegradation efficiencies of CAF and NAP when present as single compound, or as a mixture with other PhACs. Different intermediates were observed, indicating different biodegradation pathways under different redox conditions and when the PhACs were present as single compound or in a mixture. From toxicological perspective, toxicity of PhACs and/or their intermediates to Vibrio fischeri was attenuated during the biodegradation process. Chemical and toxicological data showed positive correlations in principle component analysis, by which potentially toxic PhACs and intermediates are indicated for further ecotoxicological hazard assessment.

Effects of Three Polycyclic Aromatic Hydrocarbons on Sediment Bacterial Community

Mangrove sediment is susceptible to anthropogenic pollutants, including polycyclic aromatic hydrocarbons (PAHs). However, the effects of PAHs on the bacterial diversity in mangrove sediment have been rarely studied. In the present study, the effects of three types of PAHs (Naphthalene, Fluorene, and Pyrene) at three doses on sediment microbial populations were investigated by using denaturing gradient gel electrophoresis (DGGE). After 7 and 24 days of incubation of the three types of PAHs, markedly different patterns were observed in the bacterial communities. Overall, the diversity of bacterial community was suppressed before 7 days but was promoted after 24 days. Multidimensional scaling analysis suggested that the composition of bacterial communities after 7 days was distinctly distant from that after 24 days. Also despite a slight shift of bacterial abundance, the bacterial communities were relatively steady in these sediments after exposure to PAHs. In addition, DGGE suggested that the applications of three PAHs (especially PYR) had considerable effects on bacterial communities. For phylogenetic analysis, bacteria species belonging to Proteobacteria (α-, β-, and γ-), Actinobacteria, Chloroflexi, Bacteroidetes, and Planctomycetes were changed dramatically after treatment with PAHs. These results suggest that PAHs play key roles in the change of bacterial community, which may be important for understanding the relationship between PAHs and sediment microbial ecology.

Geochemistry and Microbial Populations in Sediments of the Northern Baffin Bay, Arctic

The Northern Baffin Bay between Greenland and Canada is a remote Arctic area restricted in primary production by seasonal ice cover, with presumably low sedimentation rates, carbon content and microbial activities in its sediments. Our aim was to study the so far unknown subseafloor geochemistry and microbial populations driving seafloor ecosystems. Shelf sediments had the highest organic carbon content, numbers of Bacteria and Archaea, and microcosms inoculated from Shelf sediments showed highest sulfate reduction and methane production rates. Sediments in the central deep area and on the southern slope contained less organic carbon and overall lower microbial numbers. Similar 16S rRNA gene copy numbers of Archaea and Bacteria were found for the majority of the sites investigated. Sulfate in pore water correlated with dsrA copy numbers of sulfate-reducing prokaryotes and differed between sites. No methane was found as free gas in the sediments, and mcrA copy numbers of methanogenic Archaea were low. Methanogenic and sulfate-reducing cultures were enriched on a variety of substrates including hydrocarbons. In summary, the Greenlandic shelf sediments contain vital microbial communities adapted to their specific environmental conditions.

Effects of Alkyl Chain Branching on the Biotransformation of Naphthenic Acids

The rapid expansion of the oil sands industry has seen a concomitant expansion of the production of associated waste containing toxic naphthenic acids (NAs). Bioremediation of such waste is thus an important goal, but the mechanisms of biodegradation are still poorly understood, despite recent advances. Many oil sands NAs are resistant to biodegradation, and alkyl side chain branching has been invoked as an explanation. To investigate this hypothesis we examined the biotransformation by a sedimentary bacterial community of novel, synthetic, surrogate NAs (butylcyclohexylbutanoic acids (BCHBAs)) with variously branched butyl side chains (n- through t-) and unbranched alkanoate groups, plus one (4-(4'-isobutylcyclohexyl)pentanoic acid (iso-BCHPA)), with both branched butyl and branched alkanoate chains. Sediment microbial populations were inoculated into media containing the individual surrogate NAs, and gas chromatography-mass spectrometry (GC-MS) was used to determine the extent of biotransformation. Biotransformation decreased as NA side chain branching increased. For example, over 97% of the n-BCHBA with the nonbranched alkyl side chain was transformed in 30 days compared to the tert-BCHBA with the most highly branched side chain where only 2.5% was transformed. Both the iso-BCHBA and sec-BCHBA had intermediate transformation rates with about 77% and 47% transformed respectively after 30 days. The metabolites were identified as butylcyclohexylethanoic acids in each case, indicating beta-oxidation of the alkanoate substituents. The iso-BCHPA with both chains branched was resistant to degradation. The results are thus consistent with earlier hypotheses for the resistance of oil sands NAs. Identification of bacteria capable of oxidizing such branched alkyl chains-or of attacking the cyclic rings of NAs, may be important if bioremediation of oil sands NAs is to be achieved.

Comparison of rRNA and Polar-Lipid-Derived Fatty Acid Biomarkers for Assessment of 13 C-Substrate Incorporation by Microorganisms in Marine Sediments

We determined whether a recently developed method to isolate specific small-subunit (SSU) rRNAs can be used in 13C-labeling studies to directly link community structure and function in natural ecosystems. Replicate North Sea sediment cores were incubated at the in situ temperature following addition of 13C-labeled acetate, propionate, amino acids, or glucose. Eukaryotic and bacterial SSU rRNAs were separated from total RNA by means of biotin-labeled oligonucleotide probes and streptavidin-coated paramagnetic beads, and the 13C content of the isolated rRNA was determined by elemental analysis-isotope ratio mass spectrometry. The SSU rRNA yield with the bead-capture protocol was improved by using helper probes. Incorporation of label into bacterial SSU rRNA was detectable after 2 h of incubation. The labeling was always much greater in bacterial SSU rRNA than in eukaryotic SSU rRNA, suggesting that bacteria were the main consumers of the 13C-labeled compounds. Similar results were obtained with the 13C-labeled polar-lipid-derived fatty acid (PLFA) approach, except that more label was detected in bacterial PLFA than in bacterial SSU rRNA. This may be attributable to the generally slow growth of sediment microbial populations, which results in low ribosome synthesis rates and relatively few ribosomes per cell. We discuss possible ways to improve the probe-capture protocol and the sensitivity of the 13C analysis of the captured SSU rRNA.

Prokaryotic diversity and metabolically active microbial populations in sediments from an active mud volcano in the Gulf of Mexico

In this study, ribosomes and genomic DNA were extracted from three sediment depths (0-2, 6-8 and 10-12 cm) to determine the vertical changes in the microbial community composition and identify metabolically active microbial populations in sediments obtained from an active seafloor mud volcano site in the northern Gulf of Mexico. Domain-specific Bacteria and Archaea 16S polymerase chain reaction primers were used to amplify 16S rDNA gene sequences from extracted DNA. Complementary 16S ribosomal DNA (crDNA) was obtained from rRNA extracted from each sediment depth that had been subjected to reverse transcription polymerase chain reaction amplification. Twelve different 16S clone libraries, representing the three sediment depths, were constructed and a total of 154 rDNA (DNA-derived) and 142 crDNA (RNA-derived) Bacteria clones and 134 rDNA and 146 crDNA Archaea clones obtained. Analyses of the 576 clones revealed distinct differences in the composition and patterns of metabolically active microbial phylotypes relative to sediment depth. For example, epsilon-Proteobacteria rDNA clones dominated the 0-2 cm clone library whereas gamma-Proteobacteria dominated the 0-2 cm crDNA library suggesting gamma to be among the most active in situ populations detected at 0-2 cm. Some microbial lineages, although detected at a frequency as high as 9% or greater in the total DNA library (i.e. Actinobacteria, alpha-Proteobacteria), were markedly absent from the RNA-derived libraries suggesting a lack of in situ activity at any depth in the mud volcano sediments. This study is one of the first to report the composition of the microbial assemblages and physiologically active members of archaeal and bacterial populations extant in a Gulf of Mexico submarine mud volcano.

Mineralization of erythromycin A in aquaculture sediments

Mineralization of erythromycin A was studied using two differently 14C-labeled erythromycins A, which were added to aquaculture sediment samples obtained from the two salmon hatchery sites in Washington state. The added erythromycin A did not significantly alter the numbers of the total viable colonies and erythromycin-resistant bacteria. Erythromycin-resistant Pseudomonas species contained a constitutive erythromycin esterase activity contributing to the inactivation of biologically active erythromycin A in aquatic and sediment environments. The initial rate of mineralization of erythromycin A appeared to be governed by the rate of release of soil-sorbed erythromycin A. After a prolonged lag time, the S-curves of erythromycin A mineralization were observed probably because of the increase in the population density metabolizing it. This study suggests that erythromycin A is partially or completely mineralized by the sediment microbial populations.

Characterization of depth-related microbial community structure in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rDNA and reversely transcribed 16S rRNA fragments

Vertical changes of bacterial community structure in a mesophilic lake sediment were investigated by denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA and reversely transcribed 16S rRNA fragments. Comparison of community structure analyses based on 16S rDNA and rRNA revealed that the diversity indices from the 16S rDNA-based DGGE profiles were greater than those from the 16S rRNA-based DGGE profiles. In addition, the diversity indices based on 16S rDNA did not change drastically throughout the layers, but the diversity indices based on 16S rRNA decreased with sediment depth. This result indicates that the diversity of active bacteria decreases and inactive bacteria accumulate in association with sedimentation. Dendrograms deduced from DGGE profiles of either 16S rDNA or rRNA were different, and the rRNA-based dendrogram showed a significant difference between the upper layers (0–2, 2–5, and 5–8 cm) and lower layers (8–11, 11–14, 14–17, and 17–20 cm). The sequences of 13 DGGE bands were determined. Phylogenetic analysis of these rDNA fragments revealed that the most conspicuous band in both rDNA- and rRNA-based DGGE was closely related to the genus Nitrospira (95% sequence similarity), and the relative signal intensity was strong especially in the deep layers. Membrane hybridization with a probe targeting the genus Nitrospira also supported the observation that 16S rRNAs derived from Nitrospira-like microorganisms were abundant in this sediment (8.6–16.8% of bacterial 16S rRNA) and that the relative abundance increased with depth. Overall, our results demonstrated that parallel characterization of community structure based on both 16S rDNA and rRNA is important for assessing whole microbial populations and active microbial populations in sediments.

A comparison of sediment microbial communities associated withPhragmites australis andSpartina alterniflora in two brackish wetlands of New Jersey

The extensive spread ofPhragmites australis throughout brackish marshes on the East Coast of the United States is a major factor governing management and restoration decisions because it is assumed that biogeochemical functions are altered by the invasion. Microbial activity is important in providing wetland biogeochemical functions such as carbon and nitrogen cycling, but there is little known about sediment microbial communities inPhragmites marshes. Microbial populations associated with invasivePhragmites vegetation and with native salt marsh cordgrass,Spartina alterniflora, may differ in the relative abundance of microbial taxa (community structure) and in the ability of this biota to decompose organic substrates (community biogeochemical function). This study compares sediment microbial communities associated withPhragmites andSpartina vegetation in an undisturbed brackish marsh near Tuckerton, New Jersey (MUL), and in a brackish marsh in the anthropogenically affected Hackensack meadowlands (SMC). We use phospholipid fatty acid (PLFA) analysis and enzymataic activity to profile sediment microbial communities associated with both plants in each site. Sediment analyses include bulk density, total organic matter, and root biomass. PLFA profiles indicate that the microbial communities differ between sites with the undisturbed site exhibiting greater fatty acid richness (62 PLFA recovered from MUL versus 38 from SMC). Activity of the 5 enzymes analyzed (β-glucosidase, acid phosphatase, chitobiase, and 2 oxidases) was higher in the undisturbed site. Differences between vegetation species as measured by Principal Components Analysis were significantly greater at the undisturbed MUL site than at SMC, and patterns of enzyme activity and PLFAs did not correspond to patterns of root biomass. We suggest that in natural wetland sediments, macrophyte rhizosphere effects influence the community composition of sediment microbial populations. Physical and chemical site disturbances may impose limits on these rhizosphere effects, decreasing sediment microbial diversity and potentially, microbial biogeochemical functions.

Interactions among plant species and microorganisms in salt marsh sediments.

The interactions among Spartina patens and sediment microbial populations and the interactions among Phragmites australis and sediment microbial populations were studied at monotypic sites in Piermont Marsh, a salt marsh of the Hudson River north of New York, N.Y., at key times during the growing season. Arbuscular mycorrhizal fungi (AMF) effectively colonized S. patens but not P. australis, and there were seasonal increases and decreases that coincided with plant growth and senescence (17 and 6% of the S. patens root length were colonized, respectively). In sediment samples from the Spartina site, the microbial community and specific bacterial populations were at least twice as large in terms of number and biomass as the microbial community and specific bacterial populations in sediment samples from the Phragmites site, and peak values occurred during reproduction. Members of the domain Bacteria, especially members of the alpha-, gamma-, and delta-subdivisions of the Proteobacteria, were the most abundant organisms at both sites throughout the growing season. The populations were generally more dynamic in samples from the Spartina site than in samples from the Phragmites site. No differences between the two sites and no differences during the growing season were observed when restriction fragment length polymorphism analyses of nifH amplicons were performed in an attempt to detect shifts in the diversity of nitrogen-fixing bacteria. Differences were observed only in the patterns generated by PCR or reverse transcription-PCR for samples from the Spartina site, suggesting that there were differences in the overall and active populations of nitrogen-fixing bacteria. Regression analyses indicated that there was a positive interaction between members of the delta-subdivision of the Proteobacteria and root biomass but not between members of the delta-subdivision of the Proteobacteria and macroorganic matter at both sites. In samples from the Spartina site, there were indications that there were bacterium-fungus interactions since populations of members of the alpha-subdivision of the Proteobacteria were negatively associated with AMF colonization and populations of members of the gamma-subdivision of the Proteobacteria were positively associated with AMF colonization.

Summer abundance and activities of bacteria in the freshwater lakes of Schirmacher Oasis, Antarctica

Bacterial biomass and heterotrophic potential (using 14C-labeled glucose, glutamic acid and sodium acetate) of water, ice and sediment microbial populations were studied from different lakes of the Schirmacher Oasis, Antarctica. Epifluorescence counts of total bacteria in these lakes were observed to be lower by a factor when compared to some of the ultraoligotrophic Antarctic lakes. Biovolumes of bacteria from different samples did not show significant variations, suggesting that regulatory factors were oligotrophy and low temperatures rather than microzoan grazing. Microbial uptake rates of glutamic acid were generally the fastest, followed by glucose and/or sodium acetate in the lakewater samples. The mean values of Vmax cell−1 for glutamic acid, sodium acetate and glucose were 3.81, 0.91 and 0.71 pgCh−1. Results of this study are potentially useful in recognizing the relative abundance and activity of limnetic microbial populations in the Schirmacher Oasis during summer — the active period of microbial growth — and for comparing their activities with other ecosystems elsewhere in continental Antarctica.

Two-Stage Mineralization of Phenanthrene by Estuarine Enrichment Cultures

The polycyclic aromatic hydrocarbon phenanthrene was mineralized in two stages by soil, estuarine water, and sediment microbial populations. At high concentrations, phenanthrene was degraded, with the concomitant production of biomass and accumulation of Folin-Ciocalteau-reactive aromatic intermediates. Subsequent consumption of these intermediates resulted in a secondary increase in biomass. Analysis of intermediates by high-performance liquid chromatography, thin-layer chromatography, and UV absorption spectrometry showed 1-hydroxy-2-naphthoic acid (1H2NA) to be the predominant product. A less pronounced two-stage mineralization pattern was also observed by monitoring CO(2) production from low concentrations (0.5 mg liter) of radiolabeled phenanthrene. Here, mineralization of C-labeled 1H2NA could explain the incremental CO(2) produced during the later part of the incubations. Accumulation of 1H2NA by isolates obtained from enrichments was dependent on the initial phenanthrene concentration. The production of metabolites during polycyclic aromatic hydrocarbon biodegradation is discussed with regard to its possible adaptive significance and its methodological implications.

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 x 10 m 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.