Microbial Activity at the Sediment-Water Interface in Halifax Harbor, Canada

The sediment-water interface in Halifax Harbor supports a microbial population of 6.95 × 10⁹ cells per g (dry weight). As determined by the standard technique of suspending subsamples in filtered seawater, the uptake of added glutamic acid by this population is 113.5 ng g (dry weight)⁻¹ h⁻¹. An alternate technique was developed to measure the heterotrophic activity of the interface over longer periods of time, using undisturbed cores with the sediment-water interface intact. Under these conditions, the microbes in the water column and the interface increased exponentially in number, with mean doubling times of 9.6 and 4.5 days, respectively. The uptake of glutamic acid by the microbial population of the interface was determined to be 12.7 ng g (dry weight)⁻¹ h⁻¹, almost an order of magnitude less than the uptake determined by the previous method. This indicates that substrate diffusion and competition for substrate by the microbes in the water column are important factors when considering the heterotrophic activity of the sediment microbial population. After 48 h of incubation, uptake and respiration ceased, probably due to the exhaustion of labeled substrate. Additional substrate added after 48 h of incubation was taken up at a rate similar to that measured after the first addition. It appears that the microbial population of the interface is able to respond quickly and repeatedly to relatively large nutrient additions. After 10 days of incubation, the number of “viable” cells as determined by autoradiography was much smaller than the increase in numbers as determined by direct counts. Apparently a large part of the viable population is unaffected by nutrient addition.     

Heterotrophic Activity of Deep-Sea Sediment Bacteria

Sediment samples, containing mixed microbial populations that were decompressed during retrieval from 7,750 and 8,130 m in the Puerto Rican Trench, were recompressed and incubated at the approximate in situ temperature (3 C) and pressure (775 or 815 atm) in the presence of 14C-labeled amino acids. Heterotrophic activity (total uptake, CO2 respiration, and cellular assimilation) and cellular-associated "pool" concentrations were measured. Compared with atmospheric controls held at 3 C, the total uptake at elevated pressure at 3 C was reduced, on an average, 55 times, CO2 respiration was reduced 45 times, and cellular assimilation was reduced 69 times. Rate of total uptake at elevated pressure was found to range from 4.0 X 10(-11) mug/cell per h for leucine to 2.61 X 10(-10) mug/cell per h for an amino acid mixture. Also, the percentage of total uptake at elevated pressures, respired as CO2, increased at the expense of cellular assimilation (ca. 22% increase). Two cellular-associated amino acid pools were detected, a large, loosely bound, outer pool and a small, tightly bound internal pool. The loosely bound outer pool was removed by a change in the pH of the incubation medium. Even though heterotrophic uptake and the outer, cellular-associated pool were markedly reduced at an elevated pressure, the percentage of total uptake calculated for the unincorporated, tightly bound, intracellular pool was 2 to 19 times that obtained for cultures held at 1 atm. The results were interpreted as indicating that bacterial metabolism and biosynthesis in the deep sea are markedly reduced, with a greater proportion of metabolic activity devoted to cellular maintenance.     

Anaerobic Ammonia-Oxidizing Bacteria and Related Activity in Baltimore Inner Harbor Sediment

The discovery of bacteria capable of anaerobic ammonia oxidation (anammox) has generated interest in understanding the activity, diversity, and distribution of these bacteria in the environment. In this study anammox activity in sediment samples obtained from the Inner Harbor of Baltimore, Md., was detected by ¹⁵N tracer assays. Anammox-specific oligonucleotide primer sets were used to screen a Planctomycetales-specific 16S rRNA gene library generated from sediment DNA preparations, and four new anammox bacterial sequences were identified. Three of these sequences form a cohesive new branch of the anammox group, and the fourth sequence branches separately from this group. Denaturing gradient gel electrophoresis analysis of sediment incubated with anammox-specific media confirmed the presence of the four anammox-related 16S rRNA gene sequences. Evidence for the presence of anammox bacteria in Inner Harbor sediment was also obtained by using an anammox-specific probe in fluorescence in situ hybridization studies. To our knowledge, this is the first report of anammox activity and related bacterial 16S rRNA gene sequences from the Chesapeake Bay basin area, and the results suggest that this pathway plays an important role in the nitrogen cycle of this estuarine environment. Furthermore, the presence of these bacteria and their activity in sediment strengthen the contention that anammox-related Plactomycetales are globally distributed.     

Evaluation of Sediment Toxicity in Kaohsiung Harbor,Taiwan

The contamination and toxicity levels of sediments in Kaohsiung Harbor, Taiwan, were evaluated using different sediment quality guidelines (SQGs). Twenty dredged sediment samples were collected from various locations in the harbor. Distribution of polycyclic aromatic hydrocarbons (PAHs), heavy metals, nutrients, and total organic carbons in the sediment samples were investigated. Results from the sediment analyses show that the sediments contained significant amounts of organics, nutrients, metals, and PAHs. Based on the analyses using the SQGs, sediments dredged from Kaohsiung Harbor were moderately contaminated and most samples have a low and medium-low probability of toxicity pollution. Results show that industrial activities and urban sewage effluents are the major sources of contamination in the harbor sediments.     

Coastal Seawater Bacteria Harbor a Large Reservoir of Plasmid-Mediated Quinolone Resistance Determinants in Jiaozhou Bay, China

Diversity and prevalence of plasmid-mediated quinolone resistance determinants were investigated in environmental bacteria isolated from surface seawater of Jiaozhou Bay, China. Five qnr gene alleles were identified in 34 isolates by PCR amplification, including qnrA3 gene in a Shewanella algae isolate, qnrB9 gene in a Citrobacter freundii isolate, qnrD gene in 22 Proteus vulgaris isolates, qnrS1 gene in 1 Enterobacter sp. and 4 Klebsiella spp. isolates, and qnrS2 gene in 1 Pseudomonas sp. and 4 Pseudoalteromonas sp. isolates. The qnrC, aac(6')-Ib-cr, and qepA genes could not be detected in this study. The 22 qnrD-positive Proteus vulgaris isolates could be differentiated into four genotypes based on ERIC-PCR assay. The qnrS1 and qnrD genes could be transferred to Escherichia coli J53 Azi(R) or E. coli TOP10 recipient strains using conjugation or transformation methods. Among the 34 qnr-positive isolates, 30 had a single point mutation in the QRDRs of GyrA protein (Ala67Ser, Ser83Ile, or Ser83Thr), indicating that cooperation of chromosome- and plasmid-mediated resistance contributed to the spread and evolution of quinolone resistance in this coastal bay. Eighty-five percent of the isolates were also found to be resistant to ampicillin, and bla(CMY), bla(OXY), bla(SHV), and bla(TEM) genes were detected in five isolates that also harbored the qnrB9 or qnrS1 gene. Our current study is the first identification of qnrS2 gene in Pseudoalteromonas and Pseudomonas strains, and qnrD gene in Proteus vulgaris strains. High prevalence of diverse qnr genes in Jiaozhou Bay indicates that coastal seawater may serve as an important reservoir, natural source, and dissemination vehicle of quinolone resistance determinants.     

Diversity and Spatial Distribution of Prokaryotic Communities Along A Sediment Vertical Profile of A Deep-Sea Mud Volcano

We investigated the top 30-cm sediment prokaryotic community structure in 5-cm spatial resolution, at an active site of the Amsterdam mud volcano, East Mediterranean Sea, based on the 16S rRNA gene diversity. A total of 339 and 526 sequences were retrieved, corresponding to 25 and 213 unique (≥98% similarity) phylotypes of Archaea and Bacteria, respectively, in all depths. The Shannon–Wiener diversity index H was higher for Bacteria (1.92–4.03) than for Archaea (0.99–1.91) and varied differently between the two groups. Archaea were dominated by anaerobic methanotrophs ANME-1, -2 and -3 groups and were related to phylotypes involved in anaerobic oxidation of methane from similar habitats. The much more complex Bacteria community consisted of 20 phylogenetic groups at the phylum/candidate division level. Proteobacteria, in particular δ-Proteobacteria, was the dominant group. In most sediment layers, the dominant phylotypes of both the Archaea and Bacteria communities were found in neighbouring layers, suggesting some overlap in species richness. The similarity of certain prokaryotic communities was also depicted by using four different similarity indices. The direct comparison of the retrieved phylotypes with those from the Kazan mud volcano of the same field revealed that 40.0% of the Archaea and 16.9% of the Bacteria phylotypes are common between the two systems. The majority of these phylotypes are closely related to phylotypes originating from other mud volcanoes, implying a degree of endemicity in these systems.     

Vertical Profile of Phosphatase Activity in the Sundarban Mangrove Forest,North East Coast of Bay of Bengal,India

Impact of phosphate solubilizing bacteria along with soil phosphatase activity on phosphorous cycle was found to be quiet interesting in the Sundarban mangrove ecosystem. Soil phosphatase activity showed a decreasing pattern with increase in depth [soil phosphatase activity (μg pnp produced g^?1 dry wt of soil) = 906.85 – 5.6316 Depth (cm)] from the deep forest region of the Sundarban forest ecosystem. Soil salinity showed a very little effect on soil phosphatase activity whereas soil temperature and pH was found to show significant impact on the soil phosphatase activity. This ensured that the microbes associated with phosphate mineralization present in the Sundarban forest ecosystem are more tolerant to fluctuation in salinity than that of temperature and pH. A direct correlation was perceptible between the number of phosphate solubilizing bacteria and phosphatase activity in the soil during the study period from 2007 to 2012. Soil phosphate concentration was found to be directly governed by the soil phosphatase activity [The regression equation is: avg PO₄^?3-P (μg g^?1 dry wt of soil) = 0.0311 + 0.000606 soil phosphatase activity (μg pnp produced g^?1 dry wt of soil); R² = 63.2%, p < 0.001, n = 62].     

Sediment Distribution of Methanogenic Bacteria in Lake Erie and Cleveland Harbor

The direct fluorescent-antibody technique was employed to determine the distribution patterns of four species of methanogens in the sediments of Lake Erie and Cleveland Harbor. Methanobacterium ruminantium was the most numerous methanogen found in regions of high-organic-silt sediments. The population of this species ranged from 10⁶ to 10⁹ cells/g of dry sediment. Methanobacterium strain MoH and Methanosarcina barkeri were identified in sand-silt, clay, or sand sediments. These methanogens ranged in density from 10⁶ to 10⁷ cells/g of dry sediment. Methanospirillum hungatii was observed only after an organic enrichment was performed on Cleveland Harbor sediments. The seasonal and selective sediment distribution of these methanogens appears to be related to the type and concentration of carbon as substrate as well as to the activities of heterotrophic and sulfate-reducing bacteria.     

Respiration of Tritiated Substrates in Heterotrophic Activity Assays

The respiration percentage of ³H-labeled glucose by heterotrophic microorganisms in water samples was determined by a method based on equimolar addition of [³H]- and [¹⁴C]glucose to samples. The respiration percentage of [³H]glucose exceeded that of [¹⁴C]glucose by 10% over the assayed range of respiration rates. Respiration percentages diminished with decreasing temperature, the relation between respiration of [³H]- and [¹⁴C]glucose remaining the same. The significance of tritiated water respiration with regard to experimental design is emphasized.     

Seasonal Variation of Metals in Seawater, Sediment, and Manila Clam Ruditapes philippinarum from China

Concentrations of trace metals (Cu, Pb, Zn, Cd, Cr, Hg, and As) were determined for the first time in seawater, sediment, and Manila clam from Deer Island, Liaoning Province, China. The seawater, sediment, and clam samples were collected seasonally at three clam farming sites around Deer Island during 2010–2011. The average concentrations of Cu, Pb, Zn, Cd, Cr, Hg, and As in the seawater samples were 4.16, 0.72, 5.88, 0.45, 2.51, 0.03, and 1.02 μg/l, respectively. The seasonal variations of trace metals in seawater showed a significant difference in the concentrations of Cu, Pb, Zn, Hg, and As among seasons. The average concentrations of Cu, Pb, Zn, Cd, Cr, Hg, and As in the sediment samples were 6.43, 13.80, 53.08, 1.10, 36.40, 0.05, and 4.78 mg/kg dry weight, respectively. Trace metal concentrations in sediment seasonally varied significantly except for Cd and Hg. The average concentrations of Cu, Pb, Zn, Cd, Cr, Hg, and As in the clam samples were 11.28, 0.61, 92.50, 0.58, 3.98, 0.03, and 1.98 mg/kg dry weight, respectively. Concentrations of Cu, Zn, Cd, Cr, and As in Manila clam showed marked seasonal fluctuations with significant difference. Cu and Zn were the metals with the highest mean biosediment accumulation factor values in Manila clam. Besides, significant correlations for the concentrations of Cu and Zn relative to their concentrations in sediment were also found. Such differences in regression analyzes may be explained by differential bioaccumulation of essential and xenobiotic metals. Concentrations of trace metals in Manila clam did not exceed the maximum established regulatory concentrations for human consumption. Moreover, the calculations revealed that the estimated daily intake values for the examined clam samples were below the internationally accepted dietary guidelines and the calculated hazard quotient values were well less than 1, thus strongly indicating that health risk associated with the intake studied metals through the consumption of Manila clam from Deer Island was absent.     

Composition of Archaea in Seawater,Sediment, and Sponges in the Kepulauan Seribu Reef System,Indonesia

Coral reefs are among the most diverse and productive ecosystems in the world. Most research has, however, focused on eukaryotes such as corals and fishes. Recently, there has been increasing interest in the composition of prokaryotes, particularly those inhabiting corals and sponges, but these have mainly focused on bacteria. There have been very few studies of coral reef Archaea, despite the fact that Archaea have been shown to play crucial roles in nutrient dynamics, including nitrification and methanogenesis, of oligotrophic environments such as coral reefs. Here, we present the first study to assess Archaea in four different coral reef biotopes (seawater, sediment, and two sponge species, Stylissa massa and Xestospongia testudinaria). The archaeal community of both sponge species and sediment was dominated by Crenarchaeota, while the seawater community was dominated by Euryarchaeota. The biotope explained more than 72 % of the variation in archaeal composition. The number of operational taxonomic units (OTUs) was highest in sediment and seawater biotopes and substantially lower in both sponge hosts. No “sponge-specific” archaeal OTUs were found, i.e., OTUs found in both sponge species but absent from nonhost biotopes. Despite both sponge species hosting phylogenetically distinct microbial assemblages, there were only minor differences in Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways. In contrast, most functional pathways differed significantly between microbiomes from sponges and nonhost biotopes including all energy metabolic pathways. With the exception of the methane and nitrogen metabolic pathway, all energy metabolic pathways were enriched in sponges when compared to nonhost biotopes.     

Impact of Storms on Heterotrophic Activity of Epilimnetic Bacteria in a Southwestern Reservoir

The impact of storm conditions on the heterotrophic activity of planktonic bacteria in a southwestern reservoir was investigated. Storm events were considered as rainfall in excess of 2.5 cm in a 24-h period before sampling. Storm conditions stimulated heterotrophic activities and resulted in increased uptake rates and decreased turnover times of glutamate and acetate. Uptake rates were 45 to 75% faster immediately after storm conditions than they were during calm conditions. Activity levels appeared to return to prestorm levels within 48 h. Bacterial cell numbers did not change substantially during storm events. Cell-specific activity indicated that increases in heterotrophic activity were the result of increased activity of individual cells. Light penetration, levels of particulate organic carbon, K_t + S_n values, and population levels of attached bacteria suggest that immediate sediment loading of the reservoir or increased substrate levels could not account for abrupt increases in heterotrophic activities.     

Microcultural Study of Bacterial Size Changes and Microcolony and Ultramicrocolony Formation by Heterotrophic Bacteria in Seawater

With a microculture technique and time-lapse, phase-contrast photomicrography, it was possible to follow the division of individual cells and the development of microcolonies of bacteria in freshly collected marine water samples. A certain number of marine bacteria, upon inoculation onto a nutrient rich agar surface, displayed an increase in size as well as a high growth rate. Other bacteria were identified as very small marine bacteria (ultramicrobacteria). These had a very slow growth rate when inoculated onto a nutrient-rich agar surface. These latter cells formed very small microcolonies (ultramicrocolonies), and cell size did not increase significantly. These two types of marine heterotrophs could be described in terms of zymogenous and autochthonous bacteria, a concept used by Winogradsky for describing soil microorganisms.     

Specific Bacterial, Archaeal, and Eukaryotic Communities in Tidal-Flat Sediments along a Vertical Profile of Several Meters

The subsurface of a tidal-flat sediment was analyzed down to 360 cm in depth by molecular and geochemical methods. A community structure analysis of all three domains of life was performed using domain-specific PCR followed by denaturing gradient gel electrophoresis analysis and sequencing of characteristic bands. The sediment column comprised horizons easily distinguishable by lithology that were deposited in intertidal and salt marsh environments. The pore water profile was characterized by a subsurface sulfate peak at a depth of about 250 cm. Methane and sulfate profiles were opposed, showing increased methane concentrations in the sulfate-free layers. The availability of organic carbon appeared to have the most pronounced effect on the bacterial community composition in deeper sediment layers. In general, the bacterial community was dominated by fermenters and syntrophic bacteria. The depth distribution of methanogenic archaea correlated with the sulfate profile and could be explained by electron donor competition with sulfate-reducing bacteria. Sequences affiliated with the typically hydrogenotrophic Methanomicrobiales were present in sulfate-free layers. Archaea belonging to the Methanosarcinales that utilize noncompetitive substrates were found along the entire anoxic-sediment column. Primers targeting the eukaryotic 18S rRNA gene revealed the presence of a subset of archaeal sequences in the deeper part of the sediment cores. The phylogenetic distance to other archaeal sequences indicates that these organisms represent a new phylogenetic group, proposed as “tidal-flat cluster 1.” Eukarya were still detectable at 360 cm, even though their diversity decreased with depth. Most of the eukaryotic sequences were distantly related to those of grazers and deposit feeders.     

Lithotrophic and Heterotrophic Bacteria in Deep Subsurface Sediments and Their Relation to Sediment Properties

Subsurface sediments obtained from three cores drilled to depths of 260 m below the surface in South Carolina were analyzed for heterotrophic bacteria; N₂‐fixing microaerophiles; and nitrifying, sulfur‐oxidizing, and H₂‐oxidizing lithotrophic bacteria. In addition, pore waters were extracted for chemical analysis of inorganic nitrogen species, sulfate, dissolved organic carbon, pH, and Eh. Autotroph populations were generally less than 10³ most probable number (MPN) g^‐1 dry sediment with sulfur‐oxidizing bacteria, detected in 60% of the sediment samples, being the most frequently encountered group. Nitrifying bacteria were detected mainly in sediments from one borehole (P28), and their populations in those sediments were correlated with pore‐water ammonium concentrations. Populations of heterotrophic bacteria in 60% of the sediments were greater than 10⁶ colony forming units (CFU) g^‐1 dry sediment and were typically lower in sediments of high clay content and low pH. Microaerophilic N₂‐fixing bacteria were cultured from >50% and bacteria capable of growth on H₂ were cultured from 35% of the subsurface sediments examined. Sediment texture, which controls porosity, water potential, and hydraulic conductivity, appears to be a major factor influencing microbial populations in coastal plain subsurface sediments.     

东海洋山港沿岸土壤、海水样本中Ⅰ型PKS基因的初步筛选鉴定与功能分析

为考察土壤和海水中Ⅰ型聚酮合酶(polyketide synthase,PKS)基因的多样性和差异,本研究自行设计了一套针对PKS基因中酮缩合酶(ketosynthase,KS)片段的简并引物,使用PCR方法直接克隆东海洋山港沿岸土壤和海水DNA样本中的KS片段,去除重复序列后,共获得了23条不同的KS片段(长度为630 bp～690 bp),提交GenBank皆获登录号,其中19条来自土壤(DQ640993,DQ640997、DQ641926、DQ641927、DQ673137～DQ673151),4条来自海水(DQ673151,EF554859～EF554861),由核苷酸序列推断出的氨基酸序列保守,与GenBank中已知KS基因片段的相似度在45%到85%之间,种系发生分析表明,其中14条KS片段(来源于海水的KS片段皆在其中)应来源于典型的KS群,而剩余9条则来源于杂合的PKSmRPS(Non-ribosomalpeptide synthetase.非核糖体多肽合成酶)群.另外,几条KS基因特征明显,可用于进一步的研究.     

Influence of Cyanobacterial Hyperscum on Heterotrophic Activity of Planktonic Bacteria in a Hypertrophic Lake

The response of the planktonic heterotrophic bacterial community to the buildup and breakdown of a semipermanent, crusted, floating cyanobacterial mat, or hyperscum, that covered 1 to 2 ha was studied in a hypertrophic lake (Hartbeespoort Dam, South Africa). The initial response of bacteria in the main basin to the release of dissolved organic carbon (DOC) from the hyperscum 1 km away was an increase in activity per cell from 35 × 10⁻¹² to 153 × 10⁻¹² μg of C cell⁻¹ h⁻¹ for total cell counts, while activity per cell for metabolically active cells increased from 19 × 10⁻¹¹ to 85 × 10⁻¹¹ μg of C cell⁻¹ h⁻¹. No major population growth occurred at this stage. Later, with the continuous supply of DOC from the hyperscum, total bacterial numbers increased from 6.6 × 10⁶ to 20 × 10⁶ cells ml⁻¹, while the activity per cell declined. Metabolically active bacteria followed the same trend. Shorter-term DOC increases caused only increases in bacterial activity per cell. The data from Hartbeespoort Dam demonstrate an interesting and little-documented mechanism by which aquatic bacteria respond to increased DOC concentration and which may be universal for aquatic systems.     

Survival and Activity of lux-Marked Aeromonas salmonicida in Seawater

The fish pathogen Aeromonas salmonicida was chromosomally marked with genes encoding bacterial luciferase, luxAB, isolated from Vibrio fischeri, resulting in constitutive luciferase production. During exponential growth in liquid batch culture, luminescence was directly proportional to biomass concentration, and luminometry provided a lower detection limit of approximately 10(sup3) cells ml(sup-1), 1 order of magnitude more sensitive than enzyme-linked immunosorbent assay detection. In sterile seawater at 4(deg)C, lux-marked A. salmonicida entered a dormant, nonculturable state and population activity decreased rapidly. The activity per viable cell, however, increased by day 4, indicating that a proportion of the population remained active and culturable. Putative dormant cells were not resuscitated after the addition of a range of substrates.     

Temporal and Vertical Difference in Factors Limiting Growth Rate of Heterotrophic Bacteria in Lake Biwa

Abstract Dilution bioassays were performed to examine the seasonal and vertical difference in the relative importance of factors limiting growth of heterotrophic bacteria in Lake Biwa. The lake water diluted by 0.2 μm lake filtrate (1:6.6) was enriched either with glucose (C), inorganic phosphorus (P), ammonium nitrogen (N), amino acids (AA), or a combination of these, and incubated for 2 days at the depths where lake water was collected (2.5, 20 and 30 m depths). Experiments showed that at 2.5 m, P was the most deficient resource for bacterial growth, but the magnitude of P limitation depended on water temperature. Among others, amino acids showed a slight but significant stimulation of bacterial growth rates during the fall. At 20 and 30 m, however, growth stimulation by resource addition was rarely detected. Vertically reciprocal translocation experiments revealed that the growth rate was limited by low temperature rather than resource supply at the greater depths. The results support a simple view that bacterial growth rate is basically regulated by water temperature, but high growth rate is not realized in summer because of resource depletion. The present study suggests that both temperature and P supply play a crucial role in biogeochemical cycling of organic matter in Lake Biwa through the bacterial growth rate. Received: 10 March 1999; Accepted: 14 May 1999