The relationship between fatty acid distributions and bacterial respiratory types in contemporary marine sediments

Bacterial communities of different respiratory types were isolated from a marine sediment in a multiple chemostat system in an attempt to obtain bacterial cultures representative of the sediment. The fatty acid distribution of a mixed culture of sulphate-reducing bacteria isolated from this system showed a good correlation with the lipid distribution of the zone of maximum sulphate-reduction activity within the sediment. Both distributions had significant concentrations of C14 : 0, iso and anteiso C15 : 0, C16 : 0, C16 : 1ω7 and C18 : 1ω7. This was in contrast to the lipid profile of Desulfovibrio desulfuricans obtained by batch enrichment, which was dominated by iso C17 : 1ω7 fatty acids and correlated poorly with the sediment. The bacterial community cultured from the sediment was further differentiated according to respiratory types (aerobic, facultative aerobic and facultative anaerobic) by growth in a chemostat under defined conditions. The fatty acid distributions of these communities were sufficiently different to enable the various respiratory types to be recognized by their particular fatty acid composition. Cyclopropyl fatty acids (?17 and ?19) were present in significant levels only in the aerobic bacteria, while the facultative aerobes had significantly higher C18 : 1ω7 than the other cultures and the facultative anaerobic community was the only culture to have significant amounts of C12 : 0. The fatty acid distribution of Loch Eil sediment over the range C12-19 seemed to be predominantly of bacterial origin and were relatively abundant to a depth of 6 cm. The concentration of cyclopropyl fatty acids was highest in the oxidized surface sediments and decreased with depth as anaerobic conditions began to dominate, indicating that these fatty acids may only be indicative of aerobic sedimentary bacteria. In contrast to the fatty acids characteristic of bacteria, those fatty acids in the range C20-30 attributed to a terrestrial input were found in relatively constant concentrations over the whole 0–12 cm depth profile.     

Microbial community structure analysis of euxinic sediments using phospholipid fatty acid biomarkers

Microbial community structure in sediments, as determined by the phospholipid ester-linked fatty acid (PLFA) analysis, collected from Kojima Lake during summer and winter was described with reference to the environmental quality of the lake. A characteristic feature of the study area was the persistence of anoxia in summer and winter in the deeper area, and the sediments were under the reduced condition with high levels of sulfide, chemical oxygen demand, and low values of oxidation-reduction potential. PLFA profiles of the sediment were dominated by the saturated, branched and monounsaturated fatty acids. Small amounts (less than 5% of the total PLFA) of polyunsaturated fatty acids (biomarker fatty acids of microeukaryotes) and long chain fatty acids were detected in sediments. Total PLFA concentrations in sediments were higher in summer than in winter. Microbial community structure in the lake sediments was predominated by the prokaryotes, as evidenced from the larger amounts of bacterial biomarker fatty acids in the range of C₁₀ to C₂₀. The presence of signature fatty acids of sulfate reducing bacteria in sediments was consistent with the high levels of sulfide in the sediment and anoxic condition in the study area. PLFA showed significant differences in PLFA profiles between shallow and deeper areas, indicating the differences in the lipid contributing communities. However, no such a significant difference was observed between summer and winter.     

Microbial colonisation of artificial and deep‐sea sediments in the Arctic Ocean

Although environmental factors such as grain size and organic carbon content may influence the distribution of microbes in marine sediments, there has been little experimental study of the topic to date. To investigate how those sediment variables affect microbial colonisation under in situ conditions, deep‐sea sediments and artificial sediments (glass beads, sands) were incubated in the Arctic deep sea at 2500 m water depth with or without chitin, one of the most important carbon polymers in marine environments. Microbial abundance, biomass, chitobiase activity and changes in community structure were monitored after 7 days and 1 year. In control sediments without chitin addition, no significant changes in microbial abundance, biomass and activity were observed after 1 year. In the presence of chitin, however, considerable increases in these parameters were recorded in all three sediment types tested. Regardless of chitin addition, natural deep‐sea sediments were always associated with higher values of microbial abundance, biomass and activity compared with artificial sediments. Sediment type was always found to be the most significant factor explaining variation in enzymatic activity and bacterial community structure as compared to the effects of chitin amount, incubation time, and changes in cell number or biomass. Overall, this is the first in situ study that has addressed the effects of multiple factors and their interactions on abundance, biomass, activity and community structure of microbial communities in the deep Arctic Ocean.     

利用可提取性磷脂表征沉积物中微生物的生物量

应用ＧＣ－ＭＳ技术,分析了深圳大亚湾大鹏澳及厦门岛南岸海域沿岸几个站位沉积物中可提一磷脂酯结合态脂肪酸的含量和组成成份;同时采用吖啶橙荧光染色计数法测定了这些的中细菌的丰度、重担一。结果表明,在这些沉积物中细菌的生物量与磷脂酯结合态脂肪酸的组份的含量有着正相关关系。说明在环境生态研究中,可提取性磷脂作为海洋和河口沉积物中微生物生物量的生物标志物的可行性。     

Vegetable oil spills on salt marsh sediments; comparison between sunflower and linseed oils

The effects of a simulated spill of sunflower oil in salt marsh sediments were compared with an experiment with linseed oil. Sunflower and linseed oil penetrated the sediments at the same rates but different adsorption of the oils onto sediment particles resulted in the establishment of anaerobic conditions at shallower depths in sediments contaminated with linseed oil than with sunflower oil. The total lipid content of sunflower oil contaminated sediments remained almost stable for 6 months, whilst only 40% of linseed oil remained in the sediment after 2 months. Numbers of culturable heterotrophic bacteria and aerobic oil degrading bacteria in muddy sediment increased rapidly in response to the presence of the oils but bacterial numbers in sandy sediments increased more slowly for sunflower oil. Changes in fatty acid composition indicate similar degradation pathways for both oils but sunflower oil degraded more slowly than linseed oil and thus has the potential for longer lasting effects in marine environments.     

Seasonal distribution of bacteria in salt marsh sediments in North Carolina

The number and size of bacteria at four depths (0–1, 5–6, 10–11 and 20–21 cm) in a North Carolina salt marsh were minotored by direct counts for 13 months. The number of bacteria reached a maximum of about 1·4 × 10¹⁰ cells cm^?3 at the sediment surface in October, corresponding to the period of Spartina alterniflora die-back. Cell numbers were lowest and most consistent throughout the year at the 20 cm depth of sediment. Cell volumes averaged 0·2 μm³ at the marsh surface and decreased with depth. Mean standing crop of bacteria to a depth of 20 cm of sediment was about 14 g bacterial carbon m^?2. In surface sediments bacteria contribute up to 15% and algae up to 10% of total living microbial biomass as estimated by adenosine triphosphate (ATP). Bacteria were the major biomass component at sediment depths of 5, 10 and 20 cm. At all depths the microbial community contributes < 4% total organic carbon and < 8% of total nitrogen.     

Biochemical degradation of algal fatty acids in oxic and anoxic sediment–seawater interface systems: effects of structural association and relative roles of aerobic and anaerobic bacteria

To examine microbially mediated degradation of algal fatty acids in marine environments, we conducted a series of microcosm experiments by incubating Emiliania huxleyi cells in simulated oxic/anoxic sediment–water interface systems. Variations in concentration of fatty acids, lipid-degrading enzyme (lipase) activity, and bacterial abundance over 2-month incubations were followed to determine degradation rate constants of major algal fatty acids and responses of bacteria. In the cell-spiked experiments, fatty acids bound in the membrane and intracellular components were separated to examine effects of structural association of fatty acids on their degradation. Experimental results showed that algal fatty acids generally degraded faster (2–4×) under oxic than under anoxic conditions. Most membrane fatty acids seemed to more readily degrade than intracellular ones under anoxic conditions but the two classes degraded at similar rates under oxic conditions. Ratios of oxic to anoxic degradation rate constants were generally higher for intracellular fatty acids than for membrane fatty acids, implying that oxygen might play a more critical role in intracellular fatty acid degradation. Most algal fatty acids degraded almost completely under oxic conditions while a significant fraction (10–40%) of initially added algal fatty acids remained after 2 months under anoxic conditions. By contrast, variations in bacterial abundance during incubations were apparently greater under anoxic conditions compared to oxic conditions, suggesting that the function and relative effectiveness of aerobic vs. anaerobic bacteria rather than total bacterial abundance control biochemical degradation of algal fatty acids. Variations in potential lipase activity followed the same pattern as bacterial abundance in oxic and anoxic systems, indicating that bacteria might be a major source for lipase in these experimental systems. Bacteria-specific fatty acids varied differently during incubations and were not directly linked to bacterial abundance.     

潮间带沉积物厌氧烃降解细菌的多样性及Desulfovibrio subterraneus ND17的分离鉴定

潮间带作为海陆交界处,易受到来自海洋的石油污染,且各类石油烃进入沉积物后的降解过程尚不清楚。前人在各类生境中对好氧微生物烃降解方面已有较多研究,但对近海潮间带环境中的厌氧烃降解鲜有报道。本研究对青岛女岛湾潮间带沉积物深层样品以混合烃（中长链烷烃、多环芳烃）为碳源,硫酸盐作为电子受体进行厌氧富集培养。富集菌群的细菌多样性表明在混合烃作为碳源的作用下,优势菌群转变为脱硫叠球菌科（Desulfosarcinaceae）、脱硫杆菌科（Desulfobacteraceae）等具有石油烃降解潜力的硫酸盐还原菌。经分离纯化得到一株厌氧烃降解菌ND17,与地下脱硫弧菌属模式种Desulfovibrio subterraneus HN2T 16S rRNA基因序列的相似度为99.93%。进一步实验表明,菌株ND17在厌氧条件下对二十四烷和菲的降解率可分别达到53.9%和35.7%。这也是首次对脱硫弧菌属单菌在厌氧条件下进行石油烃降解的研究。脱硫弧菌作为一种广泛分布在厌氧环境的细菌,本研究为进一步认识其在海洋石油污染环境中的修复潜力提供了支撑。     

Metazoan meiofauna biomass, grazing, and weight-dependent respiration in the Northern Gulf of Mexico deep sea

Metazoan meiofauna are ubiquitous in marine soft sediments and play a pivotal role in diagenesis of particulate organic matter. However, the relative importance of meiofauna to the function of deep-sea benthic boundary layer communities has not been resolved. Here, meiofauna biomass, respiration, and grazing on aerobic heterotrophic bacteria were estimated and compared to standing stocks and fluxes of other benthic components (e.g., bacteria and macrofauna). Biomass and respiration declined with depth. Highest biomass and respiration occurred in the proximity of the Mississippi River on the upper continental slope of the central Gulf of Mexico. Meiofauna required 7% of their biomass per day to meet their metabolic energy budget, compared to approximately 24% day⁻¹ in shallow water. Respiration accounted for 8–22% of whole sediment community respiration (SCOC), reflecting the importance of meiofauna in diagenesis, deep-sea carbon budgets, and global biogeochemical cycles.     

Apparent Microfloral Response to Organic Degradation on Bathyal ­Seafloor: An Analysis Based on Sediment Fatty Acids

Abstract. Abyssal microfloral succession induced by experimental organic degradation was investigated. Notable changes in amounts and compositions of short-chain (C9-20) sediment fatty acids were observed, which indicated the shift of sediment microflora. Biomarker fatty acids for methanotrophs and sulfate-reducing bacteria dominated. Resultant fatty acid compositions were most closely related to those from a nearby methane seep harboring a dense Calyptogena colony; the clams were also seen in close vicinity of the deployed organic mass. These observations suggest that the organic degradation on the bathyal seafloor stimulates the formation of methanotrophic and thio­trophic microflora, resulting in the formation of a methane-seep-type benthic community.     

Microbial community respiration and structure of dead zone sediments of Omura Bay, Japan

Monitoring sediment microbial community metabolism and structure is instrumental to understanding biogeochemical processes in and ecological impacts on bottom environments. The aim of this study was to determine potential community respiration and to reveal community dynamics of the microorganisms in the dead zone sediments of Omura Bay, Japan. The bay is highly enclosed and develops severe hypoxia in the central regions every summer. We collected sediment core samples from the center of the bay during hypoxia, estimated sediment oxygen consumption by using an adapted in vivo electron transport system activity (in vivo ETSA) assay, enumerated abundance of bacteria, and analyzed bacterial community structure by automated ribosomal intergenic spacer analysis. Higher ETSA and bacterial diversity were found in upper sediments (within 3?cm depth) from the center than the fringe of the bay. Sediment bacterial community structure of the bay center was distinct from that of the fringe. From these results, upper sediment in the dead zone of Omura Bay was characterized by (1) greater community respiration and (2) greater diversity of bacterial components compared with the non-hypoxic sediment of the bay fringe. These characteristics have important implications for understanding the interaction between microbial communities and the development of hypoxia in Omura Bay.     

Lipid biomarkers for anaerobic oxidation of methane and sulphate reduction in cold seep sediments of Nyegga pockmarks (Norwegian margin): discrepancies in contents and carbon isotope signatures

Distributions and carbon isotopic compositions of microbial lipid biomarkers were investigated in sediment cores from the G11 and G12 pockmarks in the Nyegga sector of the Storegga Slide on the mid-Norwegian margin to explore differences in depth zonation, type and carbon assimilation mode of anaerobic methane-oxidizing archaea (ANMEs) and associated sulphate-reducing bacteria responsible for anaerobic oxidation of methane (AOM) in these cold seep environments. While the G11 site is characterised by black reduced sediments colonized by gastropods and Siboglinidae tubeworms, the G12 site has black reduced sediments devoid of fauna but surrounded by a peripheral occurrence of gastropods and white filamentous microbial mats. At both sites, bulk sediments contained abundant archaeal and bacterial lipid biomarkers substantially depleted in ¹³C, consisting mainly of isoprenoidal hydrocarbons and dialkyl glycerol diethers, fatty acids and non-isoprenoidal monoalkylglycerol ethers. At the G11 site, down-core profiles revealed that lipid biomarkers were in maximum abundance from 10 cm depth to the core bottom at 16 cm depth, associated with δ¹³C values of ?57 to ?136‰. At the G12 site, by contrast, lipid biomarkers were in high abundance in the upper 5 cm sediment layer, associated with δ¹³C values of ?43 to ?133‰. This suggests that, as expected from the benthic fauna characteristics of the sites, AOM takes place mainly at depth in the G11 pockmark but just below the seafloor in the G12 pockmark. These patterns can be explained largely by variable fluid flow rates. Furthermore, at both sites, a dominance of ANME-2 archaea accompanied by their bacterial partners is inferred based on lipid biomarker distributions and carbon isotope signatures, which is in agreement with recently published DNA analyses for the G11 pockmark. However, the present data reveal high discrepancies in the contents and δ¹³C values for both archaeal and bacterial lipid profiles, implying the possible involvement of at least two distinct AOM-related microbial consortia at the inferred AOM depth zonation of G11 and G12 pockmark sediments. In both sediment cores, the δ¹³C profiles for most archaeal lipids suggest a direct assimilation of dissolved inorganic carbon (DIC) in addition to methane by ANMEs (chemoautotrophy); constant and highly depleted δ¹³C profiles for PMI:3, an archaeal lipid biomarker presumably related to ANME-2, suggest a direct assimilation of ¹³C-depleted methane-derived carbon via AOM (methanotrophy). Evidently, the common approach of investigating lipid biomarker contents and δ¹³C signatures in cold seep sediments does not suffice to precisely discriminate between the carbon assimilation mode for each ANME archaeal group and associated bacteria. Rather, this needs to be combined with further specific labelling studies including different carbon sources (methane carbon, methane-derived organic intermediates and DIC) in order to unravel the metabolic pathways of each microbial consortium involved in AOM (ANME-1 vs. ANME-2 vs. ANME-3 archaeal group and associated bacteria).     

Fatty acid profiles of marine benthic microorganisms isolated from the continental slope of bay of bengal: a possible implications in the benthic Food web

Marine bacteria, actinomycetes and fungal strains were isolated from continental slope sediment of the Bay of Bengal and studied for fatty acid profile to investigate their involvement in the benthic food-web. Fifteen different saturated and unsaturated fatty acids from bacterial isolates, 14 from actinomycetes and fungal isolates were detected. The total unsaturated fatty acids in bacterial isolates ranged from 11.85 to 37.26%, while the saturated fatty acid ranged between 42.34 and 80.74%. In actinomycetes isolates, total unsaturated fatty acids varied from 27.86 to 38.85% and saturated fatty acids ranged from 35.29 to 51.25%. In fungal isolates unsaturated fatty acids ranged between 44.62 and 65.52% while saturated FA ranged from 20.80 to 46.30%. The higher percentages of unsaturated fatty acids from the microbial isolates are helpful in anticipating the active participation in the benthic food-web of Bay of Bengal.     

大连湾石油污染沉积物中细菌群落结构分析

大连新港"7.16"输油管道爆炸溢油事故发生后,为探究石油污染与细菌群落结构变化之间的关系及在石油生物降解过程中起重要作用的细菌菌群,本研究对大连湾表层沉积物中石油烃含量和细菌宏基因组16SrDNA V3区进行分析。结果表明:溢油初期2010年8月DLW01站位表层沉积物石油烃含量高达1 492mg/kg,符合第三类沉积物质量标准,随着时间推移,2011年4月、2011年7月、2011年12月航次各站位沉积物中石油烃含量基本呈下降趋势,且均符合第一类沉积物质量标准;16S rDNA PCR-DGGE方法分析表明,石油烃含量高的区域优势细菌种类少,反之则较丰富;海洋环境中同一地点的细菌群落能保持一定稳定性;大连湾石油污染沉积物中变形菌门γ-变形菌纲和拟杆菌门一直保持较高的优势度,是在石油生物降解过程中起重要作用的细菌菌群,而厚壁菌门只在石油烃含量低的区域出现;此外,出现的对污染物敏感的嗜冷杆菌可作为石油污染指示生物进行深入研究。     

Degradation of algal lipids by deep-sea benthic foraminifera: An in situ tracer experiment

We conducted an in situ feeding experiment using ¹³C-labeled unicellular algae in Sagami Bay, Japan (water depth, 1450 m), in order to understand the fate of lipid compounds in phytodetritus at the deep-sea floor. We examined the incorporation of excess ¹³C into lipid compounds extracted from bulk sediments and benthic foraminiferal cells. ¹³C-enriched fatty acids derived from ¹³C-labeled algae were exponentially degraded during 6 days of incubation in the sediment. Subsequent enrichments in ¹³C in sedimentary n-C_15, anteiso-C₁₇, and C₁₇ fatty acids indicated the microbial degradation of algal material and production of bacterial biomass in the sediment. We observed the incorporation of ¹³C-labeled algal phytol and fatty acids into foraminiferal cells. The compositions of ¹³C-labeled algal lipids in foraminiferal cells were different from those in the bulk sediments, indicating that foraminiferal feeding and digestion influenced the lipid distribution in the sediments. Furthermore, some sterols in Globobulimina affinis (e.g., 24-ethylcholesta-5,22-dien-3β-ol, 24-ethylcholest-5-en-3β-ol, and 23,24-dimethylcholesta-5,22E-dien-3β-ol) were newly produced via the modification of dietary algal sterols within 4–6 days. In addition to the effects of bacteria, feeding by benthic foraminifera can result in a significant reorganization of the composition of organic matter and influence benthic food webs and carbon cycling at the deep-sea floor.     

Microbial Diversity in Nankai Trough Sediments at a Depth of 3,843 m

Dense populations of bivalves, primarily Calyptogena sp., were observed at cold seeps of the Nankai Trough. Bacterial input to the sediment was estimated through determination of phospholipid ester-linked fatty acid (PLFA) and DNA profiles. Results indicated a bacterial biomass of 10⁹ cells (g dry wt)^-1 while individual fatty acid profiles revealed a predominance of monounsaturated fatty acids, mainly 18:1 isomers. The presence of these fatty acids can be interpreted to reflect a response to low temperature and a predominance of psychrophilic bacteria. DNA fragments encoding bacterial ribosomal RNA small-subunit sequences (16S rDNA) were amplified by the polymerase chain reaction method using DNA extracted directly from the sediment samples. From the sequencing results, at least 19 kinds of bacterial 16S rDNAs related to mostly the Proteobacteria and a few gram-positive bacteria were identified. These results suggest that the bacterial community in the Nankai Trough sediments consists of mainly bacteria belonging to the Proteobacteria , , and subdivisions. Bacteria belonging to the and subdivisions, which are known to include epibiont and sulfate reducing bacteria, respectively, were mostly detected in the sediment obtained from inside the area of the Calyptogena community, and the -Proteobacteria may function to supply reduced sulfur to bacterial endosymbionts of Calyptogena.     

Fatty acids in recent sediments in the St. Lawrence estuary

Surface sediments along the Rimouski section in the St. Lawrence estuary were sampled at the surface and at 10 cm depth. Fatty acids were extracted and analysed. Saturated and unsaturated fatty acid contents at the two depths vary with the nature of the sediments. The clay sediments rich in organic matter contain more fatty acids than the corresponding sand or gravel. Unsaturated fatty acids were more abundant in the surface sediments. Some iso- and anteiso-odd carbon fatty acids were detected in the sediments; these acids could indicate a microbial activity. Correlation is made with the fatty acid contents of the water column together with the surface microlayer of the estuarine water.     

Determination of phospholipid fatty acid structures and stable carbon isotope compositions of deep-sea sediments of the Northwest Pacific, ODP site 1179

Sediment samples ranging from 0.05 to 278 m below sea floor (mbsf) at a Northwest Pacific deep-water (5564 mbsl) site (ODP Leg 191, Site 1179) were analyzed for phospholipid fatty acids (PLFAs). Total PLFA concentrations decreased by a factor of three over the first meter of sediment and then decreased at a slower rate to approximately 30 mbsf. The sharp decrease over the first meter corresponds to the depth of nitrate and Mn(IV) reduction as indicated by pore water chemistry. PLFA-based cell numbers at site 1179 had a similar depth profile as that for Acridine orange direct cell counts previously made on ODP site 1149 sediments which have a similar water depth and lithology. The mole percentage of straight chain saturated PLFAs increases with depth, with a large shift between the 0.95 and 3.95 mbsf samples. PLFA stable carbon isotope ratios were determined for sediments from 0.05 to 4.53 mbsf and showed a general trend toward more depleted δ¹³C values with depth. Both of these observations may indicate a shift in the bacterial community with depth across the different redox zones inferred from pore water chemistry data. The PLFA 10me16:0, which has been attributed to the bacterial genera Desulfobacter in many marine sediments, showed the greatest isotopic depletion, decreasing from − 20 to − 35‰ over the first meter of sediment. Pore water chemistry suggested that sulfate reduction was absent or minimal over this same sediment interval. However, 10me16:0 has been shown to be produced by recently discovered anaerobic ammonium oxidizing (anammox) bacteria which are known chemoautotrophs. The increasing depletion in δ¹³C of 10me16:0 with the unusually lower concentration of ammonium and linear decrease of nitrate concentration is consistent with a scenario of anammox bacteria mediating the oxidation of ammonium via nitrite, an intermediate of nitrate reduction.     

渤海沉积物中细菌群落结构和基因丰度的空间分布特征

This study investigated differences in the community structure and environmental responses of the bacterial community in sediments of the Bohai Sea.Illumina high-throughput sequencing technology and real-time PCR were used to assay the bacterial 16S rRNA genes in the surface sediments of 13 sampling stations in the Bohai Sea.The results showed that sediments at the majority of the 13 sampling stations were contaminated by heavy metal mercury.The main phyla of bacteria recorded included Proteobacteria(52.92%),Bacteroidetes(11.76%),Planctomycetes(7.39%),Acidobacteria(6.53%)and Chloroflexi(4.97%).The genus with the highest relative abundance was Desulfobulbus(4.99%),which was the dominant genus at most sampling stations,followed by Lutimonas and Halioglobus.The main factors influencing bacterial community structure were total organic carbon,followed by depth and total phosphorus.The content of lead,cadmium,chromium,copper and zinc had a consistent effect on community structure.Arsenic showed a negative correlation with bacterial community structure in most samples,while the impact of mercury on community structure was not significant.The bacterial community in sediment samples from the Bohai Sea was rich in diversity and displayed an increase in diversity from high to low latitudes.The data indicated that the Bohai Sea had abundant microbial resources and was rich in bacteria with the potential to metabolize many types of pollutants.     

Evolution des hydrocarbures dans des sédiments côtiers méditerranéens prélevés à proximité d'un emissaire d'une raffinerie de pétrole

Coastal Mediterranean sediments highly polluted by refinery effluents have been studied for their hydrocarbon content and bacterial activity. The study has taken into account both the distance from the refinery and depth of sampling. Very high hydrocarbon concentrations have been found (1–250 g/kg dry sediment). Micro-organisms in the sediments have a high bacterial activity and a good correlation exists between hydrocarbon concentrations and bacteria able to use these substrates as a carbon and energy source.