Populations of Methane-Producing Bacteria and In Vitro Methanogenesis in Salt Marsh and Estuarine Sediments

Most probable numbers (MPNs) of methanogens in various salt marsh and estuarine sediments were determined with an anaerobic, habitat-simulating culture medium with 80% H₂ plus 20% CO₂ as substrate. Average MPNs for the short Spartina (SS) marsh sediments of Sapelo Island, Ga., were maximal at the 5- to 7-cm depth (1.2 × 10⁷/g of dry sediment). Populations decreased to approximately 880/g of dry sediment at the 34- to 36-cm depth. There was no significant difference between summer and winter populations. In tall Spartina (TS) marsh sediments, average populations were maximal (1.2 × 10⁶/g of dry sediment) in the upper 0- to 2-cm zone; populations from the 5- to 36-cm zones were similar (average of 9 × 10⁴/g of dry sediment). Methanogenic populations for TS sediments of James Island Creek marsh, Charleston, S.C., were similar (average of 3 × 10⁶/g of dry sediment) for all depths tested (0 to 22 cm), which was comparable to the trend observed for TS sediments at Sapelo Island, Ga. Sediment grab samples collected along a transect of James Island Creek and its adjacent Spartina marsh had MPNs that were approximately 20 times greater for the region of Spartina growth (average of 10⁶/g of dry sediment) compared with the channel (approximately 5 × 10⁴ methanogens per g of dry sediment). A similar trend was found at Pawley's Island marsh, S.C., but populations were approximately one order of magnitude lower. In vitro rates of methanogenesis with SS sediments incubated under 80% H₂-20% CO₂ showed that the 5- to 7-cm region exhibited maximal activity (51 nmol of CH₄ g⁻¹ h⁻¹), which was greater than rates for sediments above and below this depth. SS sediment samples (5 to 7 cm) incubated under 100% N₂ and supplemented with formate exhibited rates of methanogenesis similar to those generated by samples under 80% H₂-20% CO₂. Replacing the N₂ atmosphere with H₂ resulted in an eightfold decrease in the rate of methanogenesis. In vitro methanogenic activity by TS salt marsh sediments, incubated under 80% H₂-20% CO₂, was similar for all depths tested (0 to 22 cm). TS sediment samples (0 to 7 cm) supplemented with formate and incubated under 100% N₂ had greater rates of methanogenesis compared with unsupplemented samples.     

Biomass Measurement of Methanogens in the Sediments of Tokyo Bay Using Archaeol Lipids

An archaeal ether-linked lipid, archaeol, was determined to be a biomass indicator for methanogens both in the laboratory enriched culture and in marine sediments. The archaeol measurement method described by Ohtsubo et al. in 1993 was modified and applied to marine sediments. We compared the amount of archaeol with the cell number of methanogens or methane concentration in laboratory enriched culture of methanogens from marine sediment. Good correlations were obtained as follows: (Methane, mmol) = 11.2 × (Archaeol, mg): r= .996 or (Cell number) = 1.13 × 10¹¹× (Archaeol, mg): r= .995, respectively. In the sediments of Tokyo Bay, archaeol was measured from approximately 46 to 561 ng/dry g sediment at the entrance to 267 to 4160 ng/dry g sediment at the innermost area. Using the coefficient from the laboratory experiment, these data corresponded to cell numbers of 5.2 × 10⁶ to 4.7 × 10⁸/dry g sediment. These values were 1 or 2 orders of magnitude higher than those obtained by culture methods in previous studies. Although dead or decomposed cells might be detected, archaeol measurement is useful for estimating the biomass of methanogens because of the good correlation between methane concentration and archaeol content in marine environments. In this study, we found a correlation of (Methane, mmol) = 0.012 × (Archaeol, mg): r= .932, n= 17 in marine sediments. Received December 21, 1998; accepted June 16, 1999     

Effect of biostimulation on the microbial community in PCB-contaminated sediments through periodic amendment of sediment with iron

Reductive dehalogenation of polychlorinated biphenyls (PCBs) by indigenous dehalorespiring microorganisms in contaminated sediments may be enhanced via biostimulation by supplying hydrogen generated through the anaerobic corrosion of elemental iron added to the sediment. In this study, the effect of periodic amendment of sediment with various dosages of iron on the microbial community present in sediment was investigated using phospholipid fatty acid analysis (PLFA) over a period of 18 months. Three PCB-contaminated sediments (two freshwater lake sediments and one marine sediment) were used. Signature biomarker analysis of the microbial community present in all three sediments revealed the enrichment of Dehalococcoides species, the population of which was sustained for a longer period of time when the sediment microcosms were amended with the lower dosage of iron (0.01 g iron per g dry sediment) every 6 months as compared to the blank system (without iron). Lower microbial stress levels were reported for the system periodically amended with 0.01 g of iron per g dry sediment every 6 months, thus reducing the competition from other hydrogen-utilizing microorganisms like methanogens, iron reducers, and sulfate reducers. The concentration of hydrogen in the system was found to be an important factor influencing the shift in microbial communities in all sediments with time. Periodic amendment of sediment with larger dosages of iron every 3 months resulted in the early prevalence of Geobacteraceae and sulfate-reducing bacteria followed by methanogens. An average pH of 8.4 (range of 8.2–8.6) and an average hydrogen concentration of 0.75% (range of 0.3–1.2%) observed between 6 and 15 months of the study were found to be conducive to sustaining the population of Dehalococcoides species in the three sediments amended with 0.01 g iron per g dry sediment. Biostimulation of indigenous PCB dechlorinators by the periodic amendment of contaminated sediments with low dosages of iron metal may therefore be an effective technology for remediation of PCB-contaminated sediments.     

Microbial community structure and biomass estimates of a methanogenic Antarctic Lake ecosystem as determined by phospholipid analyses

Phospholipid analyses were performed on water column particulate and sediment samples from Ace Lake, a meromictic lake in the Vestfold Hills, Antarctica, to estimate the viable microbial biomass and community structure in the lake. In the water column, methanogenic bacterial phospholipids were present below 17 m in depth at concentrations which converted to a biomass of between 1 and 7×10⁸ cells/liter. Methanogenic biomass in the sediment ranged from 17.7×10⁹ cells/g dry weight of sediment at the surface to 0.1×10⁹ cells/g dry weight at 2 m in depth. This relatively high methanogenic biomass implies that current microbial degradation of organic carbon in Ace Lake sediments may occur at extremely slow rates. Total microbial biomass increased from 4.4×10⁸ cells/ liter at 2 m in depth to 19.4×10⁸ cells/liter at 23 m, near the bottom of the water column. Total nonarchaebacterial biomass decreased from 4.2 ×10⁹ cells/g dry weight in the surface sediment (1/4 the biomass of methanogens) to 0.06×10⁸ cells/g dry weight at 2 m in depth in the sediment. Phospholipid fatty acid profiles showed that microeukaryotes were the major microbial group present in the oxylimnion of the lake, while bacteria dominated the lower, anoxic zone. Sulfate-reducing bacteria (SRB) comprised 25% of the microbial population at 23 m in depth in the water column particulates and were present in the surface sediment but to a lesser extent. Biomass estimates and community structure of the Ace Lake eco-system are discussed in relation to previously measured metabolic rates for this and other antarctic and temperate ecosystems. This is the first instance, to our knowledge, in which the viable biomass of methanogenic and SRB have been estimated for an antarctic microbial community.     

The denitrification potential and density of denitrifying bacteria in the bottom sediments of Matupi Harbor (Papua New Guinea)

The denitrification potential and density of denitrifying bacteria were determined in suboxidized sediments of Matupi Harbor (Papua New Guinea). The sediments were characterized by low denitrification potentials, not exceeding 0.8 nM/(g h). The maximum density of denitrifying bacteria was recorded in the upper sediment horizons and was 10⁴ cells/g of wet ground.     

Vertical Distribution of Methanogens in the Anoxic Sediment of Rotsee (Switzerland)

Anoxic sediments from Rotsee (Switzerland) were analyzed for the presence and diversity of methanogens by using molecular tools and for methanogenic activity by using radiotracer techniques, in addition to the measurement of chemical profiles. After PCR-assisted sequence retrieval of the 16S rRNA genes (16S rDNA) from the anoxic sediment of Rotsee, cloning, and sequencing, a phylogenetic analysis identified two clusters of sequences and four separated clones. The sequences in cluster 1 grouped with those of Methanosaeta spp., whereas the sequences in cluster 2 comprised the methanogenic endosymbiont of Plagiopyla nasuta. Discriminative oligonucleotide probes were constructed against both clusters and two of the separated clones. These probes were used subsequently for the analysis of indigenous methanogens in a core of the sediment, in addition to domain-specific probes against members of the domains Bacteria and Archaea and the fluorescent stain 4′,6-diamidino-2-phenylindole (DAPI), by fluorescent in situ hybridization. After DAPI staining, the highest microbial density was obtained in the upper sediment layer; this density decreased with depth from (1.01 ± 0.25) × 10¹⁰ to (2.62 ± 0.58) × 10¹⁰ cells per g of sediment (dry weight). This zone corresponded to that of highest metabolic activity, as indicated by the ammonia, alkalinity, and pH profiles, whereas the methane profile was constant. Probes Eub338 and Arch915 detected on average 16 and 6% of the DAPI-stained cells as members of the domains Bacteria and Archaea, respectively. Probe Rotcl1 identified on average 4% of the DAPI-stained cells as Methanosaeta spp., which were present throughout the whole core. In contrast, probe Rotcl2 identified only 0.7% of the DAPI-stained cells as relatives of the methanogenic endosymbiont of P. nasuta, which was present exclusively in the upper 2 cm of the sediment. Probes Rotp13 and Rotp17 did not detect any cells. The spatial distribution of the two methanogenic populations corresponded well to the methane production rates determined by incubation with either [¹⁴C]acetate or [¹⁴C]bicarbonate. Methanogenesis from acetate accounted for almost all of the total methane production, which concurs with the predominance of acetoclastic Methanosaeta spp. that represented on average 91% of the archaeal population. Significant hydrogenotrophic methanogenesis was found only in the organically enriched upper 2 cm of the sediment, where the probably hydrogenotrophic relatives of the methanogenic endosymbiont of P. nasuta, accounting on average for 7% of the archaeal population, were also detected.     

Vertical Distribution of Ammonia-Oxidizing Archaea and Bacteria in Sediments of a Eutrophic Lake

In order to characterize the vertical variation of abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in sediments of a eutrophic lake, Lake Taihu, molecular techniques including real-time PCR, clone library, and sequencing were carried out in this study. Abundances of archaeal amoA gene (ranged from 2.34 × 10⁶ to 4.43 × 10⁷ copies [g dry sediment]^?1) were higher than those of bacterial amoA gene (ranged from 5.02 × 10⁴ to 6.91 × 10⁶ copies [g dry sediment]^?1) for all samples and both of them exhibited negative correlations with the increased depths. Diversities of archaeal and bacterial amoA gene increased with the elevated depths. There were no significant variations of AOB community structures derived from different sediment depths, whereas obvious differences were observed for the AOA community compositions. The information acquired in this study would be useful to elucidate the roles of AOA and AOB in the nitrogen cycling of freshwater ecosystems.     

Populations of Anaerobic Phototrophic Bacteria in a Spartina alterniflora Salt Marsh

Habitat-simulating media were used with the Hungate anaerobic roll tube technique to enumerate culturable anaerobic photosynthetic bacteria in sediment, tidal waters, and Spartina alterniflora plant samples collected from the salt marsh at Sapelo Island, Ga. No phototrophs were detected in samples of creekside (low marsh) sediment or in tidal waters in creekside regions. In the high marsh region, 90% of anaerobic phototrophic bacteria occurred in the top 5 mm of sediment and none were detected below 6 mm. There was a seasonal variation, with maximal populations occurring in summer and fall (mean, 4.4 × 10⁵ phototrophs g of dry sediment⁻¹) and minimal numbers occurring in winter (mean, 3.9 × 10³ phototrophs g of dry sediment⁻¹). During winter and late spring, phototrophs had a patchy distribution over the high marsh sediment surface. In contrast, during late summer they had a random uniform distribution. Tidal water collected over high marsh sediment contained an average of 8.7 × 10² phototrophs ml⁻¹, with no significant seasonal variation. Anaerobic phototrophic bacteria were also cultured from the lower stem tissue of S. alterniflora growing in both the high (4.3 × 10⁴ phototrophs g of dry tissue⁻¹) and creekside (4.9 × 10⁴ phototrophs g of dry tissue⁻¹) marsh regions. Chromatium buderi, Chromatium vinosum, Thiospirillum sanguineum, Rhodospirillum molischianum, and Chlorobium phaeobacteroides were the predominant anaerobic phototrophic species cultured from high marsh sediment. The two Chromatium species were dominant.     

Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China

We employed culture-dependent and -independent techniques to study microbial diversity in Lake Chaka, a unique hypersaline lake (32.5% salinity) in northwest China. It is situated at 3,214 m above sea level in a dry climate. The average water depth is 2 to 3 cm. Halophilic isolates were obtained from the lake water, and halotolerant isolates were obtained from the shallow sediment. The isolates exhibited resistance to UV and gamma radiation. Microbial abundance in the sediments ranged from 10⁸ cells/g at the water-sediment interface to 10⁷ cells/g at a sediment depth of 42 cm. A major change in the bacterial community composition was observed across the interface. In the lake water, clone sequences affiliated with the Bacteroidetes were the most abundant, whereas in the sediments, sequences related to low G+C gram-positive bacteria were predominant. A similar change was also present in the archaeal community. While all archaeal clone sequences in the lake water belonged to the Halobacteriales, the majority of the sequences in the sediments were related to those previously obtained from methanogenic soils and sediments. The observed changes in the microbial community structure across the water-sediment interface were correlated with a decrease in salinity from the lake water (32.5%) to the sediments (approximately 4%). Across the interface, the redox state also changed from oxic to anoxic and may also have contributed to the observed shift in the microbial community.     

Lipid composition and metabolic activities of benthic near-shore microbial communities of Arthur Harbor,antarctic peninsula: Comparisons with McMurdo Sound

Summary Benthic microbial communities of the Arthur Harbor area were described by analysis of their cell membrane phospholipid ester-linked fatty acids (PELFA) and metabolic rates. Analysis revealed a biomass averaging 6 nM (phospholipid) or 3.5×10⁸ cells per gram dry weight (gdw) of sediment for the four sites. Only slight biomass differences were detected between the four peninsula sites. All Arthur Harbor sites were determined to have a biomass similar to the lowest amount reported for a previously described McMurdo Sound site at New Harbor. Community structure based on signature phospholipids indicated only slight differences between the four peninsula sites with greater relative amounts of diatom marker lipids at a deeper site. Bacterial biomarker lipids were also determined in relatively equal proportions for the four Arthur Harbor sites with only one site indicating a somewhat decreased proportion. Metabolic rates of sodium [¹⁴C]-acetate and methyl [³H]-thymidine incorporation into lipid and bacterial DNA respectively also indicated only slight relative differences in microbial communities of Arthur Harbor study sites. Lipid metabolism (¹⁴C-acetate) ranged between 6 and 12 (x10⁴) DPM/g/h for the four sites with 8 being the average. Bacterial (excluding sulfate-reducing bacteria (SRB)) cell divisions per g per h indicated increased rates at a deeper site with 14×10⁵, compared to the average (5×10⁵) for the three remaining sites. Average estimated total bacterial (excluding SRB's) community turnover was on the order of 0.6%/h for the four sites. Metabolic rate comparisons of Arthur Harbor with those of previously determined McMurdo Sound indicated a somewhat increased lipid metabolism and an order of magnitude greater bacterial cell division rate at Arthur Harbor.This paper is part 4 in the series: Microbial Ecology in Antarctic Sea-Ice and Benthic Communities     

Life-history traits of a tube-dwelling corophioid amphipod, Paracorophium excavatum, exposed to sediment copper

This is the first demonstration that sediment contaminants can influence the reproduction of amphipods. Groups of Paracorophium excavatum from a slightly contaminated estuarine site were held within laboratory mesocosms containing four copper-spiked estuarine sediments (Cu 14-46 μg g⁻¹ dry weight) and a control sediment (Cu 5 μg g⁻¹ dry weight) at 15 °C for 28 days. Copper sediment concentration did not affect the amphipod sex ratio. Female maturation was inhibited within copper-spiked sediments but female length was similar. Juvenile recruitment occurred only in sediments containing less than 20 μg g⁻¹. Males were significantly larger than females in the control sediment (Cu 5 μg g⁻¹ dry weight) and male length decreased linearly with increasing copper concentration. The copper concentration within whole body tissues increased with dry body dry weight in all sediments except the highest copper concentration. Following 28 days of exposure, none of the female amphipods from the copper-dosed sediments was brooding embryos. In contrast, brood size of females in the control sediment (Cu 5 μg g⁻¹) was similar to field samples. Because low concentrations of sediment copper affect the maturation and growth rates of male and female amphipods differently, these life-history traits could affect the population structure of amphipods exposed to copper contaminated sediments.     

Characterization of Microbial Community Structure in the Surface Sediment of Osaka Bay, Japan, by Phospholipid Fatty Acid Analysis

Twenty-eight sediment samples collected from Osaka Bay, Japan, were analyzed for phospholipid ester-linked fatty acids (PLFA) to determine regional differences in microbial community structure of the bay. The abundance of three major groups of C₁₀ to C₁₉ PLFA (saturated, branched, and monounsaturated PLFA), which accounted for 84 to 97% of the total PLFA, indicated the predominance of prokaryotes in the sediment. The distribution of six clusters obtained by similarity analysis in the bay revealed a marked regional distribution in the PLFA profiles. Total PLFA concentrations (0.56 to 2.97 μg/g [dry weight] of the sediment) in sediments also showed marked variation among the stations, with higher concentrations of total PLFA in the central part of the bay. The biomass, calculated on the basis of total PLFA concentration, ranged from 0.25 × 10⁸ to 1.35 × 10⁸ cells per g (dry weight) of the sediment. The relative dominance of microbial groups in sediments was described by using the reported bacterial biomarker fatty acids. Very small amounts of the characteristic PLFA of microeukaryotes in sediments indicated the restricted distribution of microeukaryotes. By examining the distribution of clusters and groups of microorganisms in the bay, there were two characteristics of the distribution pattern: (i) the predominance of anaerobic bacteria and gram-positive prokaryotes, characterized by the high proportions of branched PLFA in the eastern and northeastern sides of the bay, where the reported concentrations of pollutants were also high, and (ii) the predominance of aerobic prokaryotes and eukaryotes, except for a few stations, in the western and southwestern sides of the bay, as evidenced by the large amounts of monounsaturated PLFA. Such significant regional differences in microbial community structure of the bay indicate shifts in microbial community structure.     

Composition of organic matter in sediments facing a river estuary (Tyrrhenian Sea): relationships with bacteria and microphytobenthic biomass

The relationships between the biochemical composition of sediment organic matter and bacteria and microphytobenthic biomass distribution, were investigated along the coast of Northern Tuscany (Tyrrhenian Sea). Organic matter appeared to be of highly refractory composition. Among the three main biochemical classes, proteins were the major component (0.96 mg g^-1 sediment d.w.) followed by total carbohydrates (0.81 mg g^-1 sediment d.w.) and lipids (8.1 µg g^-1 sediment d.w.). Bacterial number in surface sediments (0–2 cm) ranged from 1.7 to 24.5 × 10⁸ cells g^-1 of sediment dry weight showing a strong decrease with sediment depth. In surface sediments, significant correlations were found between bacterial biomass and protein concentration. Bacterial activity (measured by the frequency of dividing cells) was significantly related to lipid concentration. Bacterial and microphytobenthic biomass accounted for 3.1 and 18.1% respectively of the sediment organic carbon. In surface sediments bacterial lipids accounted, on average, for 27 % of total lipids, whereas bacterial proteins and carbohydrates accounted for 2.5 and 0.5% of total proteins and carbohydrates, respectively.The benthic degradation process indicated that lipids were a highly degradable compound (about 35% in the top 10 cm). Carbohydrate decreased for 25.6% in the top 10 cm, whereas proteins increased with depth, thus indicating that this compound may resist to diagenetic decomposition.These data suggest that specific organic compounds need to be measured rather than bulk carbon and nitrogen measurements in order to relate microbial biomass to the quality of organic matter.     

Characterization of the indigenous PAH-degrading bacteria of <Emphasis Type="Italic">Spartina</Emphasis> dominated salt marshes in the New York/New Jersey Harbor

The aerobic polyaromatic hydrocarbon (PAH) degrading microbial communities of two petroleum-impacted Spartina-dominated salt marshes in the New York/New Jersey Harbor were examined using a combination of microbiological, molecular and chemical techniques. Microbial isolation studies resulted in the identification of 48 aromatic hydrocarbon-degrading bacterial strains from both vegetated and non-vegetated marsh sediments. The majority of the isolates were from the genera Paenibacillus and Pseudomonas. Radiotracer studies using ¹⁴C-phenanthrene and ¹⁴C-pyrene were used to measure the PAH-mineralization activity in salt marsh sediments. The results suggested a trend towards increased PAH mineralization in vegetated sediments relative to non-vegetated sediments. This trend was supported by the enumeration of PAH-degrading bacteria in non-vegetated and vegetated sediment using a Most Probable Numbers (MPN) technique, which demonstrated that PAH-degrading bacteria existed in non-vegetated and vegetated sediments at levels ranging from 10² to 10⁵ cells/g sediment respectively. No difference between microbial communities present in vegetated versus non-vegetated sediments was found using terminal restriction fragment length polymorphism (of the 16S rRNA gene) or phospholipid fatty acid analysis. These studies provide information on the specific members and activity of the PAH-degrading aerobic bacterial communities present in Spartina-dominated salt marshes in the New York/New Jersey Harbor estuary.     

Stratification of Archaeal communities in shallow sediments of the Pearl River Estuary,Southern China

Microorganisms are known to play fundamental roles in the biogeochemical cycling of carbon in the coastal environments. To get to know the composition and ecological roles of the archaeal communities within the sediments of the Pearl River Estuary, Southern China, the diversity and vertical distribution of archaea in a sediment core was reported based on the 16S rRNA and mcrA genes for the first time. Quantitative PCR analysis revealed that archaea were present at 10⁶–10⁷ 16S rRNA gene copies/g (wet weight) in the sediment core, and the proportion of mcrA versus 16S rRNA gene copies varied from 11 to 45%. 16S rRNA gene libraries were constructed and analyzed for the top layer (0–6 cm), middle layer (18–24 cm), sulfate-methane transition zone (SMTZ, 32–42 cm), and bottom layer (44–50 cm) sediments. The results indicated that Miscellaneous Crenarchaeotal Group (MCG) was the main component in the sediments. The MCG archaea could be further divided into six subgroups: MCG-A, B, C, D, E, and F. On the other hand, mcrA sequences from methanogens related to the order Methanomicrobiales and ANME-2 methanotrophs were detected in all sediment layers. Taken together, our data revealed a largely unknown archaeal community in which MCG dominated within the Pearl River estuarine sediments, while methanogens and methane-oxidizing archaea putatively involving in methane metabolism, were also found in the community. This is the first important step towards elucidating the biogeochemical roles of these archaea in the Pearl River Estuary.     

Methyl Coenzyme M Reductase A (mcrA) Gene-Based Investigation of Methanogens in the Mudflat Sediments of Yangtze River Estuary, China

Methanogen populations of an intertidal mudflat in the Yangtze River estuary of China were investigated based on the methyl coenzyme M reductase A (mcrA) gene using 454-pyrosequencing and quantitative real-time polymerase chain reaction (qPCR). Samples were collected at six depths from three locations. In the qPCR analyses, a mean depth-wise change of mcrA gene abundance was observed from (1.23?±?0.13)×10⁷ to (1.16?±?0.29)×10⁸ per g dried soil, which was inversely correlated with the depletion of sulfate (R ²?=0.74; α?=?0.05) and salinity (R ²?=?0.66; α?=?0.05). The copy numbers of mcrA was at least 1 order of magnitude higher than dissimilatory sulfate reductase B (dsrB) genes, likely indicating the importance of methanogenesis at the mudflat. Sequences related to the orders Methanomicrobiales, Methanosarcinales, Methanobacteriales, Methanococcales and the uncultured methanogens; Rice Cluster I (RC-I), Zoige cluster I (ZC-I) and anaerobic methane oxidizing archaeal lineage-1 (ANME-1) were detected. Methanomicrobiales and Methanosarcinales dominated the entire sediment layers, but detectable changes of proportions were observed with depth. The hydrogenotrophic methanogens Methanomicrobiales slightly increased with depth while Methanosarcinales showed the reverse. Chao1 and ACE richness estimators revealed higher diversity of methanogens near the surface (0–10 cm) when compared with the bottom sediments. The near-surface sediments were mainly dominated by the family Methanosarcinaceae (45 %), which has members that can utilize substrates that cannot be used by sulfate-reducing bacteria. Overall, current data indicate that Methanosarcinales and Methanomicrobiales are the most dominant methanogens within the entire depth profile down to 100 cm, with higher abundance and diversity of methanogens in the deeper and upper sediment layers, respectively.     

Brevetoxin persistence in sediments and seagrass epiphytes of east Florida coastal waters

A bloom of Karenia brevis Davis developed in September 2007 near Jacksonville, Florida and subsequently progressed south through east Florida coastal waters and the Atlantic Intracoastal Waterway (ICW). Maximum cell abundances exceeded 10⁶ cells L⁻¹ through October in the northern ICW between Jacksonville and the Indian River Lagoon. The bloom progressed further south during November, and terminated in December 2007 at densities of 10⁴ cells L⁻¹ in the ICW south of Jupiter Inlet, Florida. Brevetoxins were subsequently sampled in sediments and seagrass epiphytes in July and August 2008 in the ICW. Sediment brevetoxins occurred at concentrations of 11–15 ng PbTx-3 equivalents (g dry wt sediment)⁻¹ in three of five basins in the northern ICW during summer 2008. Seagrass beds occur south of the Mosquito Lagoon in the ICW. Brevetoxins were detected in six of the nine seagrass beds sampled between the Mosquito Lagoon and Jupiter Inlet at concentrations of 6–18 ng (g dry wt epiphytes)⁻¹. The highest brevetoxins concentrations were found in sediments near Patrick Air Force Base at 89 ng (g dry wt sediment)⁻¹. In general, brevetoxins occurred in either seagrass epiphytes or sediments. Blades of the resident seagrass species have a maximum life span of less than six months, so it is postulated that brevetoxins could be transferred between epibenthic communities of individual blades in seagrass beds. The occurrence of brevetoxins in east Florida coast sediments and seagrass epiphytes up to eight months after bloom termination supports observations from the Florida west coast that brevetoxins can persist in marine ecosystems in the absence of sustained blooms. Furthermore, our observations show that brevetoxins can persist in sediments where seagrass communities are absent.     

Acetogenic and Sulfate-Reducing Bacteria Inhabiting the Rhizoplane and Deep Cortex Cells of the Sea Grass Halodule wrightii

Recent declines in sea grass distribution underscore the importance of understanding microbial community structure-function relationships in sea grass rhizospheres that might affect the viability of these plants. Phospholipid fatty acid analyses showed that sulfate-reducing bacteria and clostridia were enriched in sediments colonized by the sea grasses Halodule wrightii and Thalassia testudinum compared to an adjacent unvegetated sediment. Most-probable-number analyses found that in contrast to butyrate-producing clostridia, acetogens and acetate-utilizing sulfate reducers were enriched by an order of magnitude in rhizosphere sediments. Although sea grass roots are oxygenated in the daytime, colorimetric root incubation studies demonstrated that acetogenic O-demethylation and sulfidogenic iron precipitation activities were tightly associated with washed, sediment-free H. wrightii roots. This suggests that the associated anaerobes are able to tolerate exposure to oxygen. To localize and quantify the anaerobic microbial colonization, root thin sections were hybridized with newly developed ³³P-labeled probes that targeted (i) low-G+C-content gram-positive bacteria, (ii) cluster I species of clostridia, (iii) species of Acetobacterium, and (iv) species of Desulfovibrio. Microautoradiography revealed intercellular colonization of the roots by Acetobacterium and Desulfovibrio species. Acetogenic bacteria occurred mostly in the rhizoplane and outermost cortex cell layers, and high numbers of sulfate reducers were detected on all epidermal cells and inward, colonizing some 60% of the deepest cortex cells. Approximately 30% of epidermal cells were colonized by bacteria that hybridized with an archaeal probe, strongly suggesting the presence of methanogens. Obligate anaerobes within the roots might contribute to the vitality of sea grasses and other aquatic plants and to the biogeochemistry of the surrounding sediment.     

Microbial community of reduced pockmark sediments (Gdansk Deep,Baltic Sea)

The microbial community of reduced pockmark sediments in the Russian sector of the Gdansk Deep, Baltic Sea, was investigated by molecular biological techniques. Fluorescent in situ hybridization was used to determine the numbers of eubacteria, archaea, and sulfate-reducing bacteria. Eubacteria were found to predominate in the upper 10 cm of the sediment (up to 5.3 × 10⁹ cells/g wet sediment), while the number of archaea increased in the 10- to 30-cm layers (up to 2.8 × 10⁹ cells/g wet sediment, which is higher than the number of eubacteria in the same horizons). Analysis of 16S rRNA gene fragments revealed members of the following phyla: Proteobacteria, Chloroflexi, Firmicutes, Planctomycetales, and high-G + C gram-positive bacteria. Sulfate-reducing bacteria (SRBs) of the families Syntrophaceae, Desulfuromonadaceae, and Actinobacteria of the genera Kocuria and Rothia were the predominant groups. Molecular probes were used to determine predominance of Desulfovibrionales in the SRB enrichment cultures obtained from different horizons of pockmark sediments. Three archaeal phylotypes were revealed, belonging to Euryarchaeota. One of these fell into the group of uncultured methanotrophic archaea (ANME-1a), while the other two were most closely related to uncultured methanogens.