Search

We investigated the benthic foraminiferal faunal and stable carbon and oxygen isotopic composition of a 15-cm push core (NA075-092b) obtained on a Telepresence-Enabled cruise to the Southeast Seep on Kimki Ridge offshore southern California. The seep core was taken at a depth of 973 m in the vicinity of a Beggiatoa bacterial mat and vesicomyid clams ( Calyptogena ) and compared to previously published data of living assemblages from ~ 714 m, four reference cores obtained at ~ 1030 m, and another one at 739 m. All of the reference sites are also from the Inner Continental Borderland but with no evidence of methane seepage. No endemic species were found at the seep site and most of the taxa recovered there have been reported previously from other seep or low oxygen environments. Q- and R-mode cluster analyses clearly illustrated differences in the faunal assemblages of the seep and non-seep sites. The living assemblage at Southeast Seep was characterized by abundant Takayanagia delicata, Cassidulina translucens, and Spiroplectammina biformis , whereas the non-seep San Pedro Basin reference assemblage was comprised primarily of Chilostomella oolina and Globobulimina pacifica . Density and species richness were lower at the seep site compared to the non-seep site, reflecting the harsher living conditions there. The dead assemblage at the seep site was dominated by Gyroidina turgida compared to Cassidulina translucens at the ~ 1030 m non-seep site and Cassidulina translucens, Pseudoparrella pacifica, and Takayanagia delicata at the 739 m non-seep site. Density was three times lower at Southeast Seep than at the non-seep sites of comparable water depth but species richness was ~ 30% higher. Stable carbon isotopic values were considerably depleted in the seep samples compared to the non-seep samples, with a progression from lightest to heaviest average δ 13 C values evident at the seep site reflecting microhabitat preference and vital effect: the deep infaunal species of Globobulimina , the shallow infaunal species Uvigerina peregrina , the epifaunal species Cibicidoides wuellerstorfi , and the shallow infaunal but aragonite-shelled species Hoeglundina elegans . The δ 13 C values downcore among each benthic species indicates ongoing fluid seepage through at least the last 3800 cal yr B.P. at Southeast Seep. Besides the continual local seepage, evidence from δ 13 C values of planktic foraminifera in the seep core suggest two pulses of methane (at 3000 and 3700 cal yr B.P.) were released that were large enough to influence much of the water column. Paired benthic and planktic foraminiferal stable oxygen isotope records provide evidence that there were no paleoenvironmental changes such as increased bottom-water temperature or changes in oxygen isotopic composition of bottom and pore waters during this 3800-year record to induce the methane releases. Instead, Southeast Seep appears to be the result of local faulting providing pathways for fluid to flow to the seafloor at a fault stepover or transpressional bend in the regional strike-slip system. [ABSTRACT FROM AUTHOR]

Finfish aquaculture can be installed over hard and patchy substrates where grab sampling is challenging and use of video can be an appropriate tool to document benthic changes. Video monitoring can show visual indicators of enrichment, namely flocculent matter, Beggiatoa -like mats, and opportunistic polychaete complexes (OPC). We examined factors influencing presence of indicators using 52 video monitoring reports collected in Newfoundland, Canada. The main driving factor was distance to cage, with indicators showing a higher probability of occurrence within 10 m from cages due to low current velocities. Indicators were less prevalent on sites dominated by hard substrates while OPC in particular were restricted to depths > 35 m. Beggiatoa- like bacteria covered a larger surface than the two other indicators; however, our results suggest the necessity of amalgamating information related to all the indicators (including bare stations that could indicate anoxia) to establish a more accurate evaluation of aquaculture impact. [ABSTRACT FROM AUTHOR]

The colourless mat covering organically enriched sediments underlying an intensive salmon farm in Estero Pichicolo, southern Chile, was surveyed by combined 454 PyroTag and conventional Sanger sequencing of 16S/18S ribosomal RNA genes for Bacteria and Eukarya . The mat was dominated by the sulphide-oxidizing bacteria (SOB) Candidatus Isobeggiatoa, Candidatus Parabeggiatoa and Arcobacter . By order of their abundances, sulphate-reducing bacteria (SRB) were represented by diverse deltaproteobacterial Desulfobacteraceae , but also within Desulfobulbaceae , Desulfuromonadaceae and Desulfovibrionaceae . The eukaryotic PyroTags were dominated by polychaetes, copepods and nematodes, however, ciliated protozoans were highly abundant in microscopy observations, and were represented by the genera Condylostoma , Loxophyllum and Peritromus . Finally, the abundant Sulfurimonas / Sulfurovum also suggest the occurrence of zero-valence sulphur oxidation, probably derived from Beggiatoaceae as a result of bacteriovorus infaunal activity or generated as free S 0 by the Arcobacter bacteria. The survey suggests an intense and complex sulphur cycle within the surface of salmon-farm impacted sediments. [ABSTRACT FROM AUTHOR]

The photoactivated cyclase bPAC of the microbial mats bacterium Beggiatoa sp. consists of a BLUF domain and an adenylyl cyclase domain. It has strong activity of photo-induced cyclic adenylyl monophosphate (cAMP) formation and is therefore an important optogenetic tool in neuroscience applications. The SUMO-bPAC-Y7F mutant where Tyr-7 is replaced by Phe-7 in the BLUF domain has lost the typical BLUF domain photo-cycle dynamics. Instead, the investigated SUMO-bPAC-Y7F mutant consisted of three protein conformations with different triplet based photo-dynamics: (i) reversible flavin quinone (Fl) cofactor reduction to flavin semiquinone (FlH ), (ii) reversible violet/near ultraviolet absorbing flavin photoproduct (FlA) formation, and (iii) irreversible red absorbing flavin photoproduct (FlC) formation. Absorption and emission spectroscopic measurements on SUMO-bPAC-Y7F were carried out before, during and after light exposure. Flavin photo-dynamics schemes are developed for the SUMO-bPAC-Y7F fractions performing photo-induced FlH , FlA, and FlC formation. Quantitative parameters of the flavin cofactor excitation, relaxation and recovery dynamics in SUMO-bPAC-Y7F are determined. [ABSTRACT FROM AUTHOR]

Abstract: Sulfide-oxidizing bacteria of the genus Beggiatoa are found in conspicuous, colorful mats on the seafloor above active hydrothermal seeps at Guaymas Basin. Guaymas Beggiatoa filaments fall into discrete size classes representing at least five separate 16S rRNA phylotypes, and appear either white, yellow, or orange. During two R/V Atlantis cruises to Guaymas Basin, 78 temperature profiles were taken near and within 15 different orange and white Beggiatoa mats by the Alvin submersible to investigate spatial relationships between mat color and hydrothermal fluid seeps, as indicated by elevated temperatures. The surface temperatures from 78 profiles are similar to each other (on average 8–12°C, warmer than bare sediments at 3–4°C), indicating that Guaymas Basin Beggiatoa spp., although relying on the hydrothermal system for energy and carbon sources, live within a relatively cool temperature range. Temperatures from 40cm below orange Beggiatoa versus white Beggiatoa are the same, at 84°C averaged across all mat systems. However, within a single mat system, temperatures are higher beneath the predominantly orange center of the mat than beneath the white mat periphery. Push core transects across the orange-to-white color change of three Beggiatoa mats showed stronger upward compression of isotherms and metabolic zones beneath the orange mat center than beneath white mat periphery. Hydrothermal temperature gradients push the microbial processes generating carbon and energy sources for Beggiatoa mats towards the sediment surface. The resulting steep gradients of hydrothermal electron donors and carbon sources to the sediment surface, rather than the in situ temperature by itself, control the relative positioning of orange and white filaments within a Guaymas Basin Beggiatoa mat. Given the wide spectrum of temperature and hydrothermal flux regimes between different mats, the orange/white pattern represents a relative preference or even a competitive balance among different Beggiatoa types that establishes itself within each hydrothermal hot spot. [Copyright &y& Elsevier]

Abstract: Beggiatoa species are filamentous sulfide-oxidizing bacteria belonging to the family Beggiatoaceae that contains several largest bacteria known today. These large sulfur bacteria occur in diverse ecosystems and play an important role in the global sulfur, nitrogen and phosphorus cycle. In this study, sediment samples from brackishwater shrimp culture ponds and other brackishwater ecosystems from Tamil Nadu, southeast coast of India, were enriched for Beggiatoa species. Extracted hay medium supplemented with catalase was used and were incubated for two weeks at 28°C. Out of seven set-ups, four yielded positive growth of filamentous sulfide-oxidizing bacteria. The filaments were several millimeters long, ranged in width between 2 and 15μm and exhibited typical gliding motility. The 16S rRNA gene of four single filaments representing the four positive enrichments was subjected to PCR-DGGE followed by sequencing. All four filaments were affiliated to the Beggiatoaceae, but showed less than 89% identity with the Beggiatoa type strain Beggiatoa alba and less than 93% identity with any other sequence of the family. One of the four filaments revealed a nearly full-length 16S rDNA sequence (1411bp) and it formed a monophyletic cluster with two of the partial DGGE-16S rRNA gene sequences (99–100% identity) within the Beggiatoa species cluster. These organisms could possibly represent a novel genus within the family Beggiatoaceae. The fourth partial sequence affiliated with less than 93% sequence identity to the genera Parabeggiatoa, Thioploca and Thiopilula, and was likewise strongly delineated from any sequence published in the family. [Copyright &y& Elsevier]

Abstract: The seven Messinian microbial carbonate-rich layers cropping out in the Pollenzo section (Tertiary Piedmont Basin, NW Italy) are interbedded with a precession-related cyclic succession composed of euxinic shale/marl couplets and straddle the onset of the Messinian salinity crisis (MSC). A sharp change of sedimentological, compositional and geochemical characteristics was observed from the onset of the MSC onward, suggesting strong differences in the mechanisms responsible for carbonate precipitation. Pre-MSC beds are mainly composed of dolomite and are interpreted as the product of early diagenesis, formed by bacterial sulphate reduction in the shallow subsurface along the sulphate–methane interface. Dolomite precipitation was temporarily enhanced by an upward flux of methane-rich fluids, possibly sourced by gas hydrate destabilisation. Conversely, from the onset of the MSC onward, carbonate beds are thinly laminated and show abundant filaments interpreted as Beggiatoa-like bacteria, while calcite (and aragonite) are the dominant authigenic phases. These beds are interpreted as microbialites, resulting from the lithification of chemotrophic bacterial mats dominated by sulphide-oxidizing bacteria. The carbonate necessary for their preservation was provided by bacterial sulphate reduction. These microbialites, that appear as the deeper water counterpart of bottom-grown selenite layers deposited in the marginal part of the basin, formed on an anoxic sea bottom under a density stratified water column. The high sulphate concentration in the pore waters, related to the presence of concentrated brines and to the regeneration of sulphate by sulphide-oxidizing bacteria, is considered as the driving factor controlling the mineralogical change from dolomite to calcite and aragonite. Finally, the sharp shift towards negative δ18O values of carbonates, observed from the onset of the MSC onward, was probably related to fractionation processes operated by sulphate-reducing bacterial communities in the pore waters. This suggests that care must be taken, when dealing with microbial carbonates, in the interpretation of the oxygen isotope values in terms of fluctuating salinity condition of the water mass. In conclusion, this study suggests that the onset of the MSC had a strong impact on microbial populations governing carbonate precipitation, in a sector of the basin dominated by depositional conditions not suitable for gypsum precipitation. [Copyright &y& Elsevier]

Abstract: The colorless, large sulfur bacteria are well known because of their intriguing appearance, size and abundance in sulfidic settings. Since their discovery in 1803 these bacteria have been classified according to their conspicuous morphology. However, in microbiology the use of morphological criteria alone to predict phylogenetic relatedness has frequently proven to be misleading. Recent sequencing of a number of 16S rRNA genes of large sulfur bacteria revealed frequent inconsistencies between the morphologically determined taxonomy of genera and the genetically derived classification. Nevertheless, newly described bacteria were classified based on their morphological properties, leading to polyphyletic taxa. We performed sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions, together with detailed morphological analysis of hand-picked individuals of novel non-filamentous as well as known filamentous large sulfur bacteria, including the hitherto only partially sequenced species Thiomargarita namibiensis, Thioploca araucae and Thioploca chileae. Based on 128 nearly full-length 16S rRNA-ITS sequences, we propose the retention of the family Beggiatoaceae for the genera closely related to Beggiatoa, as opposed to the recently suggested fusion of all colorless sulfur bacteria into one family, the Thiotrichaceae. Furthermore, we propose the addition of nine Candidatus species along with seven new Candidatus genera to the family Beggiatoaceae. The extended family Beggiatoaceae thus remains monophyletic and is phylogenetically clearly separated from other related families. [Copyright &y& Elsevier]

Abstract: Understanding biological rhythms in benthic ecosystems and their modulation by habitat cycles has important implications for resource and ecosystem management. The recent development of permanent, multi-sensor seafloor observatories in deep-water environments provides opportunities for the in situ investigation of the behaviour of benthic organisms in relation to habitat variability. This paper describes a multi-disciplinary investigation at the VENUS observatory platform in Saanich Inlet, an intermittently anoxic fjord (Vancouver Island, Canada). A remotely operated digital camera (103m depth) was used to document changes in the abundance of shrimp (Spirontocaris spp.) and the squat lobster (Munida quadrispina), as well as bacterial mat coverage (Beggiatoa spp.). These data were used as proxies of diel rhythms related to day–night and internal tidal cycles. Seafloor photos were acquired hourly during consecutive days, before, during and after oxygen intrusion events in the fall of 2009. In order to relate biological fluctuations to habitat cycles, bottom water pressure, temperature, dissolved oxygen, and nitrate data were also acquired from the observatory database. Periodogram analysis showed a weak internal-tide-associated rhythmicity for Spirontocaris spp. that was absent in M. quadrispina and in bacterial mat coverage. Waveform analysis confirmed the absence of any day–night fluctuation in all tested species. However, a rapid intrusion of oxygenated water at the study site influenced visual counts of species, possibly blurring detectable activity rhythms. Temperature and nitrate fluctuations were more accentuated during spring tides but cross-correlation analysis indicated an absence of species responses to these habitat variables. Results are discussed within the context of the complex oceanographic dynamics of Saanich Inlet and with respect to understanding the ecological consequences of expanding hypoxia in the global ocean. [Copyright &y& Elsevier]

Abstract: The main criterion to classify a microorganism as belonging to the genus Beggiatoa is its morphology. All multicellular, colorless, gliding bacterial filaments containing sulfur globules described so far belong to this genus. At the ultrastructural level, they show also a very complex cell envelope structure. Here we describe uncultured vacuolated and non-vacuolated bacteria from two different environments showing all characteristics necessary to assign a bacterium to the genus Beggiatoa. We also intended to investigate whether narrow and vacuolate Beggiatoa do differ morphologically as much as they do phylogenetically. Both large, vacuolated trichomes and narrow filaments devoid of vacuoles were observed. We confirmed the identity of the narrow filaments by 16S rRNA phylogenetic analysis. The diameters of the trichomes ranged from 2.4 to 34μm, and their lengths ranged from 10μm to over 30mm. Narrow trichomes moved by gliding at 3.0μm/s; large filaments moved at 1.5μm/s. Periplasmic sulfur inclusions were observed in both types of filaments, whereas phosphorus-rich bodies were found only in narrow trichomes. On the other hand, nitrate vacuoles were observed only in large trichomes. Ultra-thin section transmission electron microscopy showed differences between the cell ultrastructure of narrow (non-vacuolated) and large (vacuolated) Beggiatoa. We observed that cell envelopes from narrow Beggiatoa consist of five layers, whereas cell envelopes from large trichomes contain four layers. [Copyright &y& Elsevier]

Abstract: Imaging techniques that allow intracellular pH determination in ranges below pH 3 employ costly equipment and can have a long data acquisition time (minutes). Here, we describe a new methodology based on excited state saturation employing the fluorophore fluorescein-iso-thio-cyanate for confocal microscopy allowing a fast data acquisition in live organisms. To develop the method a model description of the fluorophore''s molecular states was developed that led to a ratio function dependant on the excited states'' lifetime. Due to the lifetime dependence on the pH of dissolved fluorescein-iso-thio-cyanate this ratio function was useful for pH determination. The model was tested theoretically and the pH dependence of the ratio function was verified experimentally with an artificial dye-bead system. Finally, a simple measuring protocol was developed allowing the automatic determination of the ratio function in images of live cells under the confocal microscope. This procedure was applied successfully to vacuolated Beggiatoa filaments with different internal pH values, near neutral in the cytoplasm and acidic in the vacuoles. [Copyright &y& Elsevier]

Abstract: The high Antarctic marine system, including McMurdo Sound, is food limited. Benthic scavengers, especially the seastar Odontaster validus, respond rapidly to sources of organic material, however, fecal material from the McMurdo Station sewage outfall is not consumed. Laboratory and field experiments showed that O. validus responded quickly (within hours) to organically enriched sediments, but that the presence of the anaerobic bacteria Beggiatoa spp. modified seastar behavior. In the lab, anoxic sediments, even more strongly than the presence of Beggiatoa, caused seastar avoidance. In the field, Beggiatoa caused seastar avoidance even of organically enriched sediments. The large mass of organic material remaining from pre-sewage treatment years at the McMurdo outfall is currently completely covered by a thick Beggiatoa microbial mat. O. validus and other megafaunal scavengers are abundant nearby but do not feed on the sewage organics that are covered by the microbes. The outfall deposit is thus likely to exist for a long period of time, undergoing slow anaerobic microbial degradation rather than rapid processing by megafaunal scavengers. This is an example of competition between constituents of the microbial and megafaunal communities and espouses the need for an ecosystem approach to ecology rather than community analysis within a limited size class (i.e. mega-, macro-, meio-, or micro-fauna). [Copyright &y& Elsevier]

Abstract: Assemblages of live (Rose-Bengal-stained) and dead benthic foraminifera and stable oxygen and carbon isotopic composition of live benthic foraminifera were studied in and outside a bacterial mat composed of the large sulphur-oxidizing bacteria Thioploca and Beggiatoa from the oxygen-minimum zone off Pakistan (NE Arabian Sea). Two cores from the same Multicorer retrieved a bacterial mat and ambient sediment. The dominant species (Globobulimina affinis, G. turgida, Bolivina pacifica, B. pseudopunctata, Uvigerina peregrina and Buliminella tenuata) in both cores are characteristic for dysoxic oxygen minimum zone conditions. The most significant difference between the two cores is the reduced number of stained benthic foraminifera (SBF) in the top 0.5cm of the bacterial mat. Faunal densities of stained species are more than four times higher in the sediment surface sample (0–0.5cm) outside the bacterial mat, at a distance of only 1.5m. All stained species, however, observed outside the Beggiatoa/Thioploca mat were also observed in the core with the mat. Two species, Virgulinella fragilis and Bolivina dilatata, occur exclusively in the core with the bacterial mat. The diversity within the bacterial mat core is thus slightly higher than outside. Furthermore, the abundances of the species Buliminella morgani, B. tenuata and Alliatina primitiva are substantially higher in the bacterial mat than outside. Globobuliminids, on the other hand, seem to prefer the conditions outside the bacterial mat and are five times more frequent in the core taken outside the bacterial mat. Benthic foraminifers inhabit a broader microhabitat range outside the bacterial mat (∼5cm) than within (3.5cm). A marked decrease in SBF abundances was observed at the level of a black sulphur-rich layer which is interpreted to mark the shallow redox front below the bacterial mat. Stable carbon isotope analyses on live benthic foraminifera do not support a relation of the investigated Beggiatoa/Thioploca mat to a constant or seasonal seepage of methane at the continental slope off Pakistan. Surprisingly, however, stable oxygen isotope values of many species and especially of U. peregrina decrease with depth, which calls into question the suitability of U. peregrina as a recorder of bottom-water δ 18O. [Copyright &y& Elsevier]

We determined the geochemical characteristics of sediments and measured rates of the anaerobic oxidation of methane (AOM) and sulfate reduction (SR) in samples collected near thermogenic (structure II) gas hydrate mounds and in areas lacking hydrates along the continental slope in the Gulf of Mexico. We used radiotracer (C-14 and S-35) techniques to determine rates of AOM and SR over depth in sediment cores. Abundant mats of white and orange Beggiatoa spp. were common in areas of active seepage and these sediments were enriched in hydrogen sulfide and methane. In cores collected from areas without Beggiatoa or hydrate, concentrations of redox metabolites showed little variation over depth and these sites were inferred to be areas of low seepage. Integrated AOM rates were low in Beggiatoa-free cores (<0.05 mmol m−2 day−1) and averaged 2.8±4.6 mmol m−2 day−1 in seep cores that contained Beggiatoa or gas hydrate. Integrated SR rates were also low in Beggiatoa-free cores (<1 mmol m−2 day−1) and averaged 54±94 mmol m−2 day−1 in cores with Beggiatoa or hydrate. Rates of SR generally exceeded rates of AOM and the two processes were loosely coupled, suggesting that the majority of SR at Gulf of Mexico hydrocarbon seep sites is likely fueled by the oxidation of other organic matter, possibly other hydrocarbons and oil, rather than by AOM. [Copyright &y& Elsevier]

Nitrate-accumulating filamentous bacteria from organic rich sediment of Tokyo Bay, morphologically similar to Beggiatoa species, were phylogenetically analyzed. From several sites in Tokyo Bay, Beggiatoa-like bacteria were collected. Each sample contained narrower or wider type (10 and 30 μm, respectively) of trichomes. With the nested PCR using specific primers for Beggiatoa, fragments of 16S rRNA gene were amplified and then subjected to denaturing gradient gel electrophoresis (DGGE) analysis. Sequencing and the following phylogenetic analysis indicated that they are related to large Beggiatoa species. The wider type was related to uncultured Beggiatoa clones of other geographical localities and distinct from the narrower type in Tokyo Bay. Among the narrower types, a sample from a tidal flat was genetically distinct from the sample from sites of 10 and 20 m water depth. These narrower types form a new branch in Beggiatoa/Thioploca cluster. The result of phylogenetic analysis was in accordance with the previous studies that indicate possession of nitrate-accumulation capability is congruent with phylogeny based on 16S rRNA sequences. [Copyright &y& Elsevier]