Leaching: use of a thermophilic and chemoautotrophic microbe.

PubMed

Brierley, C L; Murr, L E

1973-02-02

A chemoautotrophic, thermophilic, and acidophilic microorganism capable of oxidizing reduced sulfur and iron compounds and leaching concentrates of molybdenite and chalcopyrite at 60 degrees C has been characterized by transmission and scanning electron microscopy. This constitutes the first direct observations of microorganisms on ore fines.

Discovery of chemoautotrophic symbiosis in the giant shipworm Kuphus polythalamia (Bivalvia: Teredinidae) extends wooden-steps theory.

PubMed

Distel, Daniel L; Altamia, Marvin A; Lin, Zhenjian; Shipway, J Reuben; Han, Andrew; Forteza, Imelda; Antemano, Rowena; Limbaco, Ma Gwen J Peñaflor; Tebo, Alison G; Dechavez, Rande; Albano, Julie; Rosenberg, Gary; Concepcion, Gisela P; Schmidt, Eric W; Haygood, Margo G

2017-05-02

The "wooden-steps" hypothesis [Distel DL, et al. (2000) Nature 403:725-726] proposed that large chemosynthetic mussels found at deep-sea hydrothermal vents descend from much smaller species associated with sunken wood and other organic deposits, and that the endosymbionts of these progenitors made use of hydrogen sulfide from biogenic sources (e.g., decaying wood) rather than from vent fluids. Here, we show that wood has served not only as a stepping stone between habitats but also as a bridge between heterotrophic and chemoautotrophic symbiosis for the giant mud-boring bivalve Kuphus polythalamia This rare and enigmatic species, which achieves the greatest length of any extant bivalve, is the only described member of the wood-boring bivalve family Teredinidae (shipworms) that burrows in marine sediments rather than wood. We show that K. polythalamia harbors sulfur-oxidizing chemoautotrophic (thioautotrophic) bacteria instead of the cellulolytic symbionts that allow other shipworm species to consume wood as food. The characteristics of its symbionts, its phylogenetic position within Teredinidae, the reduction of its digestive system by comparison with other family members, and the loss of morphological features associated with wood digestion indicate that K. polythalamia is a chemoautotrophic bivalve descended from wood-feeding (xylotrophic) ancestors. This is an example in which a chemoautotrophic endosymbiosis arose by displacement of an ancestral heterotrophic symbiosis and a report of pure culture of a thioautotrophic endosymbiont.

Gene flow between Atlantic and Pacific Ocean basins in three lineages of deep-sea clams (Bivalvia: Vesicomyidae: Pliocardiinae) and subsequent limited gene flow within the Atlantic

NASA Astrophysics Data System (ADS)

LaBella, Abigail Leavitt; Van Dover, Cindy L.; Jollivet, Didier; Cunningham, Clifford W.

2017-03-01

Pliocardiin (vesicomyid) clams rely on microbial symbionts for nutrition and are obligate inhabitants of deep-sea chemosynthetic ecosystems. Unlike many other invertebrate hosts of chemosynthetic microbes, pliocardiin clams are found in every ocean in a variety of reducing habitats, including hydrothermal vents, cold seeps, organic falls and deep-sea fans. The global distribution of pliocardiin clams suggests historical gene flow between ocean basins. We focus on 3 pliocardiin genera-'Pliocardia' I, Calyptogena and Abyssogena-each of which has a pair of sister clades in the Atlantic and Pacific. Our work tests the hypothesis that historical gene flow between the Atlantic and Pacific Oceans within these genera was interrupted by the closure of the Panamanian seaway and tests whether isolation between the ocean basins is the result of vicariance or past colonization. These questions are investigated in the context of fossil evidence, biogeography and phylogenetics. This study revealed a set of substitution rates consistent with other invertebrate studies (μ=0.8%/My/lineage), and a set consistent with much lower rates often attributed to deep-sea organisms (μ=0.3%/My/lineage). Among the Pacific/Atlantic sister pairs, 'Pliocardia' I COI divergence per lineage is intermediate (2.5%), Calyptogena is the highest (6.1%) and Abyssogena the lowest (0.8%). The substitution rates suggest that 'Pliocardia' I and Calyptogena have histories of at least 2.8 My in the Atlantic, with Calyptogena likely older. The slower rate, however, is inconsistent with both the maximum age of the family and several well studied fossils: leaving the faster rate preferred. With the faster rate, the Abyssogena southwardae clade diverged from its Pacific sister clade around 1 Mya, which likely post-dates the closure of the Isthmus of Panama and the opening of the Bering Strait. In light of this recent divergence, we test the previously proposed hypothesis that there is a high level of ongoing gene flow between Atlantic populations of A. southwardae. A. southwardae has colonized a broad geographic range of seep sites including the West Florida Escarpment, the Barbados Accretionary Prism, the Lobes of Congo, and the Mid-Atlantic Ridge north and south of the Romanche Transform Fault. Coalescent methods detect gene flow between Barbados and the Mid-Atlantic ridge; and between the West Florida Escarpment and the Lobes of Congo. All other comparisons failed to detect gene flow, contrary to prevailing interpretations of connectivity across the entire Atlantic Basin.

Discovery of chemoautotrophic symbiosis in the giant shipworm Kuphus polythalamia (Bivalvia: Teredinidae) extends wooden-steps theory

PubMed Central

Altamia, Marvin A.; Lin, Zhenjian; Shipway, J. Reuben; Han, Andrew; Forteza, Imelda; Antemano, Rowena; Limbaco, Ma. Gwen J. Peñaflor; Dechavez, Rande; Albano, Julie; Rosenberg, Gary; Concepcion, Gisela P.; Schmidt, Eric W.; Haygood, Margo G.

2017-01-01

The “wooden-steps” hypothesis [Distel DL, et al. (2000) Nature 403:725–726] proposed that large chemosynthetic mussels found at deep-sea hydrothermal vents descend from much smaller species associated with sunken wood and other organic deposits, and that the endosymbionts of these progenitors made use of hydrogen sulfide from biogenic sources (e.g., decaying wood) rather than from vent fluids. Here, we show that wood has served not only as a stepping stone between habitats but also as a bridge between heterotrophic and chemoautotrophic symbiosis for the giant mud-boring bivalve Kuphus polythalamia. This rare and enigmatic species, which achieves the greatest length of any extant bivalve, is the only described member of the wood-boring bivalve family Teredinidae (shipworms) that burrows in marine sediments rather than wood. We show that K. polythalamia harbors sulfur-oxidizing chemoautotrophic (thioautotrophic) bacteria instead of the cellulolytic symbionts that allow other shipworm species to consume wood as food. The characteristics of its symbionts, its phylogenetic position within Teredinidae, the reduction of its digestive system by comparison with other family members, and the loss of morphological features associated with wood digestion indicate that K. polythalamia is a chemoautotrophic bivalve descended from wood-feeding (xylotrophic) ancestors. This is an example in which a chemoautotrophic endosymbiosis arose by displacement of an ancestral heterotrophic symbiosis and a report of pure culture of a thioautotrophic endosymbiont. PMID:28416684

Traumatic myiasis agents in Iran with introducing of new dominant species, Wohlfahrtia magnifica (Diptera: Sarcophagidae)

PubMed Central

Rafinejad, Javad; Akbarzadeh, Kamran; Rassi, Yavar; Nozari, Jamasp; Sedaghat, Mohammad Mehdi; Hosseini, Mostafa; Alipour, Hamzeh; Ranjbar, Abdolmajid; Zeinali, Danial

2014-01-01

Objective To study agents of animal wound myiasis in various geographical districts of Fars province. Methods This study has been done in Fars province, located in the southern part of Iran. Sums of 10 358 domestic animals have been visited from April 2011 to March 2012. The infected wounds in any parts of animal body were sampled by means of forceps. Results About 61% of all animal wound myiasis were caused by larvae of Wohlfahrtia magnifica. The most wound myiasis cases due to this species occurred in central part of Fars province. There wasn't any significant difference between sheep and goat in infestation with myiasis (P>0.05). The infestation rate of myiasis in cattle community was 0.86%. Conclusions The infestation rate of livestock was lower than other works in Iran and some other countries like Saudi Arabia. Chrysomya bezziana has been mentioned as main myiasis agent in Iran. But in this study it cleared that similarly to some European countries, the common animal myiasis agent in Iran is Wohlfahrtia magnifica. Introducing new species as principal agent for myiasis can help public health and animal husbandry policy makers to prepare sufficient and effective control and/or preventive measures for this disease. PMID:25182946

Diversity of Total Bacterial Communities and Chemoautotrophic Populations in Sulfur-Rich Sediments of Shallow-Water Hydrothermal Vents off Kueishan Island, Taiwan.

PubMed

Wang, Li; Cheung, Man Kit; Liu, Rulong; Wong, Chong Kim; Kwan, Hoi Shan; Hwang, Jiang-Shiou

2017-04-01

Shallow-water hydrothermal vents (HTVs) are an ecologically important habitat with a geographic origin similar to that of deep-sea HTVs. Studies on shallow-water HTVs have not only facilitated understanding of the influences of vents on local ecosystems but also helped to extend the knowledge on deep-sea vents. In this study, the diversity of bacterial communities in the sediments of shallow-water HTVs off Kueishan Island, Taiwan, was investigated by examining the 16S ribosomal RNA gene as well as key functional genes involved in chemoautotrophic carbon fixation (aclB, cbbL and cbbM). In the vent area, Sulfurovum and Sulfurimonas of Epsilonproteobacteria appeared to dominate the benthic bacterial community. Results of aclB gene analysis also suggested involvement of these bacteria in carbon fixation using the reductive tricarboxylic acid (rTCA) cycle. Analysis of the cbbM gene showed that Alphaproteobacterial members such as the purple non-sulfur bacteria were the major chemoautotrophic bacteria involving in carbon fixation via the Calvin-Benson-Bassham (CBB) cycle. However, they only accounted for <2% of the total bacterial community in the vent area. These findings suggest that the rTCA cycle is the major chemoautotrophic carbon fixation pathway in sediments of the shallow-water HTVs off Kueishan Island.

Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils.

PubMed

Long, Xi-En; Yao, Huaiying; Wang, Juan; Huang, Ying; Singh, Brajesh K; Zhu, Yong-Guan

2015-06-16

Previous studies suggested that microbial photosynthesis plays a potential role in paddy fields, but little is known about chemoautotrophic carbon fixers in drained paddy soils. We conducted a microcosm study using soil samples from five paddy fields to determine the environmental factors and quantify key functional microbial taxa involved in chemoautotrophic carbon fixation. We used stable isotope probing in combination with phospholipid fatty acid (PLFA) and molecular approaches. The amount of microbial (13)CO2 fixation was determined by quantification of (13)C-enriched fatty acid methyl esters and ranged from 21.28 to 72.48 ng of (13)C (g of dry soil)(-1), and the corresponding ratio (labeled PLFA-C:total PLFA-C) ranged from 0.06 to 0.49%. The amount of incorporationof (13)CO2 into PLFAs significantly increased with soil pH except at pH 7.8. PLFA and high-throughput sequencing results indicated a dominant role of Gram-negative bacteria or proteobacteria in (13)CO2 fixation. Correlation analysis indicated a significant association between microbial community structure and carbon fixation. We provide direct evidence of chemoautotrophic C fixation in soils with statistical evidence of microbial community structure regulation of inorganic carbon fixation in the paddy soil ecosystem.

Methods and systems for chemoautotrophic production of organic compounds

DOEpatents

Fischer, Curt R.; Che, Austin J.; Shetty, Reshma P.; Kelly, Jason R.

2013-01-08

The present disclosure identifies pathways, mechanisms, systems and methods to confer chemoautotrophic production of carbon-based products of interest, such as sugars, alcohols, chemicals, amino acids, polymers, fatty acids and their derivatives, hydrocarbons, isoprenoids, and intermediates thereof, in organisms such that these organisms efficiently convert inorganic carbon to organic carbon-based products of interest using inorganic energy, such as formate, and in particular the use of organisms for the commercial production of various carbon-based products of interest.

Methods and systems for chemoautotrophic production of organic compounds

DOEpatents

Fischer, Curt R.; Che, Austin J.; Shetty, Reshma P.; Kelly, Jason R.

2018-02-27

The present disclosure identifies pathways, mechanisms, systems and methods to confer chemoautotrophic production of carbon-based products of interest, such as sugars, alcohols, chemicals, amino acids, polymers, fatty acids and their derivatives, hydrocarbons, isoprenoids, and intermediates thereof, in organisms such that these organisms efficiently convert inorganic carbon to organic carbon-based products of interest using inorganic energy, such as formate, and in particular the use of organisms for the commercial production of various carbon-based products of interest.

Response to comment on “The conundrum between chemoautotrophic production and reductant and oxidant supply: A case study from the Cariaco basin”

NASA Astrophysics Data System (ADS)

Li, Xiaona; Taylor, Gordon T.; Astor, Yrene; Varela, Ramon; Scranton, Mary I.

2012-12-01

Jost (in press) argued that our measured chemoautotrophic production is overestimated due to methodology and that oxygen contamination is the most likely explanation for the energy conundrum. We have endeavored to minimize atmospheric exposure from sample collection through incubation since the CARIACO program began. We have also intentionally added headspaces to examine the aeration effect and found that, if anything, oxygen contamination appears to suppress 14C fixation rates at the depths of interest. Even if trace oxygen contamination occurs during sample preparation and incubation, we do not believe that could explain the 800 to1600-fold difference between the chemoautotrophic production and the reactant supply using stoichiometry based on lab cultures of sulfide oxidizers. In Li et al. (2012), the stoichiometry we used does not violate any thermodynamic laws. Thus the value we used, while probably on the high side, is theoretically possible. We argue that production of sulfide within the redoxcline may be a significant source based on the fact that a large fraction of the organic matter produced by the chemoautotrophs within the redoxcline does not seem to settle into underlying sediment traps. Our main intention was to propose that in situ sulfide production, i.e., a “cryptic sulfur cycle”, within the redoxcline might be a significant, but neglected process.

Chemoautotrophic carbon fixation rates and active bacterial communities in intertidal marine sediments.

PubMed

Boschker, Henricus T S; Vasquez-Cardenas, Diana; Bolhuis, Henk; Moerdijk-Poortvliet, Tanja W C; Moodley, Leon

2014-01-01

Chemoautotrophy has been little studied in typical coastal marine sediments, but may be an important component of carbon recycling as intense anaerobic mineralization processes in these sediments lead to accumulation of high amounts of reduced compounds, such as sulfides and ammonium. We studied chemoautotrophy by measuring dark-fixation of 13C-bicarbonate into phospholipid derived fatty acid (PLFA) biomarkers at two coastal sediment sites with contrasting sulfur chemistry in the Eastern Scheldt estuary, The Netherlands. At one site where free sulfide accumulated in the pore water right to the top of the sediment, PLFA labeling was restricted to compounds typically found in sulfur and ammonium oxidizing bacteria. At the other site, with no detectable free sulfide in the pore water, a very different PLFA labeling pattern was found with high amounts of label in branched i- and a-PLFA besides the typical compounds for sulfur and ammonium oxidizing bacteria. This suggests that other types of chemoautotrophic bacteria were also active, most likely Deltaproteobacteria related to sulfate reducers. Maximum rates of chemoautotrophy were detected in first 1 to 2 centimeters of both sediments and chemosynthetic biomass production was high ranging from 3 to 36 mmol C m(-2) d(-1). Average dark carbon fixation to sediment oxygen uptake ratios were 0.22±0.07 mol C (mol O2)(-1), which is in the range of the maximum growth yields reported for sulfur oxidizing bacteria indicating highly efficient growth. Chemoautotrophic biomass production was similar to carbon mineralization rates in the top of the free sulfide site, suggesting that chemoautotrophic bacteria could play a crucial role in the microbial food web and labeling in eukaryotic poly-unsaturated PLFA was indeed detectable. Our study shows that dark carbon fixation by chemoautotrophic bacteria is a major process in the carbon cycle of coastal sediments, and should therefore receive more attention in future studies on sediment biogeochemistry and microbial ecology.

7 CFR 301.92-2 - Restricted, regulated, and associated articles; lists of proven hosts and associated plant taxa.

Code of Federal Regulations, 2012 CFR

2012-01-01

... willow *Sequoia sempervirens Coast redwood *Syringa vulgaris Lilac *Taxus baccata European yew... Phytophthora ramorum: Abies concolor White fir Abies grandis Grand fir Abies magnifica Red fir Acer circinatum...

7 CFR 301.92-2 - Restricted, regulated, and associated articles; lists of proven hosts and associated plant taxa.

Code of Federal Regulations, 2013 CFR

2013-01-01

... willow *Sequoia sempervirens Coast redwood *Syringa vulgaris Lilac *Taxus baccata European yew... Phytophthora ramorum: Abies concolor White fir Abies grandis Grand fir Abies magnifica Red fir Acer circinatum...

7 CFR 301.92-2 - Restricted, regulated, and associated articles; lists of proven hosts and associated plant taxa.

Code of Federal Regulations, 2014 CFR

2014-01-01

... willow *Sequoia sempervirens Coast redwood *Syringa vulgaris Lilac *Taxus baccata European yew... Phytophthora ramorum: Abies concolor White fir Abies grandis Grand fir Abies magnifica Red fir Acer circinatum...

7 CFR 301.92-2 - Restricted, regulated, and associated articles; lists of proven hosts and associated plant taxa.

Code of Federal Regulations, 2010 CFR

2010-01-01

... willow *Sequoia sempervirens Coast redwood *Syringa vulgaris Lilac *Taxus baccata European yew... Phytophthora ramorum: Abies concolor White fir Abies grandis Grand fir Abies magnifica Red fir Acer circinatum...

7 CFR 301.92-2 - Restricted, regulated, and associated articles; lists of proven hosts and associated plant taxa.

Code of Federal Regulations, 2011 CFR

2011-01-01

... willow *Sequoia sempervirens Coast redwood *Syringa vulgaris Lilac *Taxus baccata European yew... Phytophthora ramorum: Abies concolor White fir Abies grandis Grand fir Abies magnifica Red fir Acer circinatum...

Fir dwarf mistletoe (FIDL).

Treesearch

Gregory M. Filip; Jerome S. Beatty; Robert L. Mathiasen

2000-01-01

Fir dwarf mistletoe (Arceuthobium abietinum Engelmann ex Munz) is a common and damaging parasite of white fir (Abies concolor (Gord. & Glend.) Lindl. ex Hildebr.), grand fir (Abies grandis (Dougl. ex D. Don) Lindl.), and California red fir (A. magnifica A. Murr.) in the western...

Genetic tools link long-term demographic and life-history traits of anemonefish to their anemone hosts

NASA Astrophysics Data System (ADS)

Salles, Océane C.; Saenz-Agudelo, Pablo; Almany, Glenn R.; Berumen, Michael L.; Thorrold, Simon R.; Jones, Geoffrey P.; Planes, Serge

2016-12-01

The life-history traits and population dynamics of species are increasingly being attributed to the characteristics of their preferred habitats. While coral reef fish are often strongly associated with particular habitats, long-term studies establishing the demographic and life-history consequences of occupying different reef substrata are rare and no studies have monitored individuals in situ over their lifetime and determined the fate of their offspring. Here, we documented a quasi-turnover and local reproductive success for an entire population of orange clownfish ( Amphiprion percula) from Kimbe Island, Papua New Guinea, by taking bi-annual samples of DNA over a 10-yr period (2003-2013). We compared demographic and life-history traits of individuals living on two host anemone species, Heteractis magnifica and Stichodactyla gigantea, including female size, adult continued presence (a proxy for relative longevity range), early post-settlement growth, the number of eggs per clutch and `local' reproductive success (defined for each adult as the number of offspring returning to the natal population). Our results indicate that while the relative longevity of adults was similar on both host anemone species, females living in H. magnifica were larger than females in S. gigantea. However, despite females growing larger and producing more eggs on H. magnifica, we found that local reproductive success was significantly higher for clownfish living in S. gigantea. Life-history traits also exhibited local spatial variation, with higher local reproductive success recorded for adults living on S. gigantea on the eastern side of the island. Our findings support a `silver-spoon' hypothesis that predicts individuals that are fortunate enough to recruit into good habitat and location will be rewarded with higher long-term reproductive success and will make a disproportionate contribution to population renewal.

Hybridization of a Rocky Mountain fir (Abies concolor) and a Mexican fir (Abies religiosa).

Treesearch

J.B. St. Clair; W.B. Critchfield

1988-01-01

Interspecific crosses of Abies religiosa (HBK.) Schlecht. & Cham. (oyamel) with Abies concolor (Gord. & Glend.) Lindle. ex Hildebr. var. concolor (white fir) and Abies magnifica A. Murr. (California red fir) were undertaken to explore the relationships between these species. The...

Hybridization of a Rocky Mountain fir (Abies concolor) and a Mexican fir (Abies religiosa)

Treesearch

J. B. St. Clair; W. B. Critchfield

1988-01-01

Interspecific crosses of Abies religiosa (HBK.) Schlecht. & Cham, (oyamel) with Abies concolor (Gord. & Glend.) Lindl. ex Hildebr. var. concolor (white fir) and Abies magnifica A. Murr. (California red fir) were undertaken to explore the relationships between these species. The cross...

Estimation of past intermittent methane seep activity using radiocarbon dating of Calyptogena shells in the eastern Nankai subduction zone

NASA Astrophysics Data System (ADS)

Yagasaki, K.; Ashi, J.; Yokoyama, Y.; Miyairi, Y.; Kuramoto, S.

2013-12-01

Radioisotope carbon dating samples from the deep ocean has always been a difficult phenomenon due to the carbon offset present. This research presents a way of utilizing such method to date shell samples in order to study past fault activities. The research presented will be based on the preliminary data collected thus far. The Nankai and the Tokai regions are common areas for cold seeps, where seepage of hydrogen sulfide and methane rich fluid occurs. These various substances encourage the growth of Calyptogena colonies to flourish at these sites. Cold seeps generally occur at tectonically active continental margins and are mostly ephemeral. This suggests that the cold seep events are possibly influenced by the tectonic activity during the plate divergence. In 1997, a submersible dive by Shinkai 2000 discovered an unusually large Calyptogena colony ranging over 200 m2 off Daini Tenryu Knoll. Majority of the shells were fossilized with few live shells remaining. It is assumed that past tectonic events in the region may have caused a high flux of methane fluid or gas to be released, making it possible to support such a vast scale colony to survive until their eventual death. Previous attempt to reconstruct the cold seep activity history through amino acid racemisation dating revealed two different age grouped shells. Further data using a different method is required to prove its reliability, as acid racemization dating technique can easily be affected by seawater temperature changes and microbial activity. This consequently alters the protein structure of the sample and its overall age. As 14C radioisotope dating is not affected by temperature change, it will provide additional information to the accuracy of the acid racemisation dating of the shell. However, the possibility of contamination is likely due to the shells incorporating older carbon from the sediments during their early stages of growth. The old carbon value can be calculated by subtracting the formerly alive shell age away from the fossilsed shell age. Preliminary results of radiocarbon dating indicate a distinct age gap of several hundred years between the formerly alive shells (~ 1126calAD -1276calAD) and the fossil shells (~ 671calAD - 797calAD).

Dwarf Mistletoe on Red Fir . . . infection and control in understory stands

Treesearch

Robert F. Scharpf

1969-01-01

Height and age of understory red fir (Abies magnifica A. Murr.) were related to dwarf mistletoe (Arceuthobiilm campylopodum f. abietinum) infection from the surrounding overstory red fir on four National Forests in California. Percentage of trees infected and intensity of infection increased significantly as height of understory...

Rooting cuttings from douglas-fir, white-fir, and California red fir christmas trees

Treesearch

C. M. Blankensop; R. Z. Callaham

1960-01-01

Christmas tree growers in California have asked geneticists to help improve the characteristics of the - wild species they are cultivating. The preferred Christmas trees of California are Shasta red fir (Abies magnifica A. Murr.), white fir (A. concolor (Gord. & Glend.) Lindl.), and Douglas-fir (Pseudotsuga...

Population dynamics of dwarf mistletoe on young true firs in the central Sierra Nevada, California

Treesearch

Robert E Scharpf; J. R. Jr. Parmeter

1982-01-01

Young red firs (Abies magnifica A. Murr.) and white firs (A. concolor [Gord. & Glend.] Lindl. ex Hildebr.) on the Stanislaus National Forest, California, were inoculated with seeds of dwarf mistletoe (Arceuthobium abietinum) for 5 successive years. Only 3 to 4 percent of about 7000 seeds placed on branches...

Grayback Glades Research Natural Area: guidebook supplement 49

Treesearch

Reid Schuller; Bryan Wender; Rachel Showalter

2016-01-01

This guidebook describes major biological and physical attributes of the 433-ha (1,070-ac) Grayback Glades Research Natural Area. The area supports high- elevation examples of white fir–Shasta red fir (Abies concolor[Gord. + Glend]–Abies magnifica var. shastensis) forest along the crest of the Siskiyou...

Nest trees of northern flying squirrels in the Sierra Nevada

Treesearch

Marc D. Meyer; Douglas A. Kelt; Malcolm P. North

2005-01-01

We examined the nest-tree preferences of northern flying squirrels (Glaucomys sabrinus) in an old-growth, mixed-conifer and red fir (Abies magnifica) forest of the southern Sierra Nevada of California. We tracked 27 individuals to 122 nest trees during 3 summers. Flying squirrels selected nest trees that were larger in diameter and...

Growth of California red fir advance regeneration after overstory removal and thinning

Treesearch

William W. Oliver

1985-01-01

Advance regeneration is common under decadent, old-growth stands of California red fir (Abies magnifica A. Murr.). Intense competition for the site's resources can create sapling stands of poor vigor and advanced age. When competition is reduced by overstory removal and thinning, suppressed advance regeneration has been shown to respond with...

Early verification of a hybrid between noble and California red firs

Treesearch

Roy R. Silen; William B. Critchfield; Jerry F. Franklin

1965-01-01

Hybrids between Abies procera Rehd., and Abies magnifica A. Murr., made reciprocally at Marys Peak near Corvallis, Oreg., and near Placerville, Calif., suggest that no significant genetic barriers prevent crossing of the two species where ranges overlap. Hence, maintenance of species differences must be looked for in other factors...

Spatial and Temporal Population Genetics at Deep-Sea Hydrothermal Vents Along the East Pacific Rise and Galapagos Rift

DTIC Science & Technology

2008-09-01

locality and moment in time. The present composition of alleles within a population establishes its future course of persistence or extinction, adaptation ...Calyptogena magnified NEPR, GAR 3,340 17,n,c 0.016 No5’’ nonplanktotrophic"’ short Gastropods Eulepetop.si.s vilrea NEPR, GAR 3,340 10 0.059 No...Massachusetts Institute of Technology/Woods Hole Oceanographic Institution, MA. Adams DK, Mullineaux LS (2008) Supply of gastropod larvae to hydrothermal vents

Decay losses associated with wounds in commercially thinned true fir stands in northern California.

Treesearch

Paul E. Aho; Gary Fiddler; Gregory M. Filip

1989-01-01

A total of 562 white firs (Abies concolor (Gord. & Glend.) Lindl. ex Hildebr.) and red firs (A. magnifica A. Murr.) with logging wounds were felled, dissected, and analyzed for infection and decay in 28 commercially thinned stands on the Klamath and Tahoe National Forests in California. On the Klamath National Forest, decay...

Mortality and growth of dwarf mistletoe-infected red and white fir and the efficacy of thinning for reducing associated losses

Treesearch

H. K. Mehl; S. R. Mori; S. J. Frankel; D. M. Rizzo

2013-01-01

In managed forests dominated by true fir (Abies) species, stands are often restocked using understory trees retained during timber harvest, making the effects of dwarf mistletoe (Arceuthobium spp.) infestation on small true fir a concern. This study examined the response of small red (A. magnifica) and...

Ten-year risk-rating systems for California red fir and white fir: development and use

Treesearch

George T. Ferrell

1989-01-01

Logistic regression equations predicting the probability that a tree will die from natural causes--insects, diseases, intertree competition--within 10 years have been developed for California red fir (Abies magnifica) and white fir (A. concolor). The equations, like those with a 5-year prediction period already developed for these...

Dwarf mistletoe in red and white firs in California–23 to 28 years after inoculation

Treesearch

John R. Parmeter Jr.; Robert F. Scharpf

1989-01-01

Spread and buildup of dwarf mistletoe, Arceuthobium abietinum, was studied on inoculated white fir, Abies concolor, and red fir, A. magnifica, in northern California for 23 to 28 years. At the end of these studies (1986), and in the absence of overstory infection, 13 of 23 trees had dwarf mistletoe populations...

Chamaebatia foliolosa Benth.: bearmat

Treesearch

Arthur W. Magill; Susan E. Meyer

2008-01-01

Two varieties of this species - Chamaebatia foliolosa Benth. - are recognized. The typical variety, bearmat, is an evergreen shrub, 15 to 60 cm tall, that grows between 600 and 2,100 m elevation on the western slopes of the Sierra Nevada in California. It occurs in open ponderosa pine (Pinus ponderosa Dougl. ex Laws.) and in California red fir (Abies magnifica A. Murr...

Heart Rots of Red and White Firs

Treesearch

J.W. Kimmey; H.H. Jr. Bynum

1961-01-01

Heart rots, caused by fungi that attack the heartwood of living trees, are responsible for the greatest volume loss sustained by California red fir (Abies magnifica A. Murr.) and white fir (A. concolor (Gord. and Glend.) Lindl.). These two firs comprise 25 percent of the commercial timber of California. More than 13 percent of the volume in these firs is useless cull...

Paracatenula, an ancient symbiosis between thiotrophic Alphaproteobacteria and catenulid flatworms

PubMed Central

Gruber-Vodicka, Harald Ronald; Dirks, Ulrich; Leisch, Nikolaus; Stoecker, Kilian; Bulgheresi, Silvia; Heindl, Niels Robert; Horn, Matthias; Lott, Christian; Loy, Alexander; Wagner, Michael; Ott, Jörg

2011-01-01

Harnessing chemosynthetic symbionts is a recurring evolutionary strategy. Eukaryotes from six phyla as well as one archaeon have acquired chemoautotrophic sulfur-oxidizing bacteria. In contrast to this broad host diversity, known bacterial partners apparently belong to two classes of bacteria—the Gamma- and Epsilonproteobacteria. Here, we characterize the intracellular endosymbionts of the mouthless catenulid flatworm genus Paracatenula as chemoautotrophic sulfur-oxidizing Alphaproteobacteria. The symbionts of Paracatenula galateia are provisionally classified as “Candidatus Riegeria galateiae” based on 16S ribosomal RNA sequencing confirmed by fluorescence in situ hybridization together with functional gene and sulfur metabolite evidence. 16S rRNA gene phylogenetic analysis shows that all 16 Paracatenula species examined harbor host species-specific intracellular Candidatus Riegeria bacteria that form a monophyletic group within the order Rhodospirillales. Comparing host and symbiont phylogenies reveals strict cocladogenesis and points to vertical transmission of the symbionts. Between 33% and 50% of the body volume of the various worm species is composed of bacterial symbionts, by far the highest proportion among all known endosymbiotic associations between bacteria and metazoans. This symbiosis, which likely originated more than 500 Mya during the early evolution of flatworms, is the oldest known animal–chemoautotrophic bacteria association. The distant phylogenetic position of the symbionts compared with other mutualistic or parasitic Alphaproteobacteria promises to illuminate the common genetic predispositions that have allowed several members of this class to successfully colonize eukaryote cells. PMID:21709249

Anomalous δ13C in POC at the chemoautotrophy maximum in the Cariaco Basin

NASA Astrophysics Data System (ADS)

Scranton, M. I.; Taylor, G. T.; Thunell, R.; Tappa, E.; benitez-Nelson, C. R.; Muller-Karger, F. E.; Lorenzoni, L.; Astor, Y. M.

2016-02-01

The Cariaco Basin is the world's largest truly marine, permanently anoxic basin and is located on the continental shelf of Venezuela which experiences strong seasonal upwelling. The CARIACO program has been studying the hydrography, biogeochemistry and properties of sinking flux of the Cariaco Basin since 1995. One of the major puzzles of CARIACO has been the nature of the chemoautotrophic maximum which is seen at depths just below the appearance of hydrogen sulfide ( 250-300 m). The identity and sources of oxidants and reductants to this active microbial community, and the identity of the chemoautotrophic organisms themselves, are still only partially known. Below about 50m (the euphotic zone), δ13C values of suspended particulates range from -23 to -26‰, typical of marine phytoplankton. However we have observed both enrichments (values of up to -16‰) and depletions (values of -28‰) near the redox interface. We had expected to see isotopically light POC in the chemoautotrophy maximum, since DIC δ13C should decrease with depth as organic carbon is remineralized. However both positive and negative isotopic excursions in POC occur at depths where dark carbon fixation is at a maximum, and at or near the transition from micro-oxic to sulfidic water. We postulate that this signal may help to define carbon fixation pathways (and dominant chemoautotrophic populations) in the oxic/sulfidic transition region.

Large Vesicomyidae (Mollusca: Bivalvia) from cold seeps in the Gulf of Guinea off the coasts of Gabon, Congo and northern Angola

NASA Astrophysics Data System (ADS)

von Cosel, Rudo; Olu, Karine

2009-12-01

Two new genera and three new species of large Vesicomyidae are described from cold-seep sites on pockmarks and other sulfide-rich environments in the Gulf of Guinea (tropical east Atlantic) off Gabon, Congo (Brazzaville) and northern Angola, from 500 to 4000 m depth: " Calyptogena" (s.l.) regab n. sp., Wareniconcha (n.g.) guineensis (Thiele and Jaeckel 1931), Elenaconcha guiness n.g. n. sp., and Isorropodon atalantae n. sp. For two other species already taken by the R/V Valdivia in 1898, Calyptogena valdiviae (Thiele and Jaeckel 1931) and Isorropodon striatum (Thiele and Jaeckel 1931) new localities were discovered, and the species are rediscussed. E. guiness n.g. n.sp. is also recorded from off Banc d'Arguin, Mauritania, collected by commercial fishing vessels. The vesicomyid species here treated were encountered in different depth ranges along the Gabon-Congo-Angola margin, between 500 and 4000 m depth, and it was found that, in comparison with the dredge samples taken by the Valdivia expedition off southern Cameroon and off Rio de Oro (both at 2500 m), the same species occur in other depth ranges, in some cases with a vertical difference of more than 1000 m. .That means that the species are not confined to a given depth thought being typical for them and that the characteristics of the biotope are likely to play a major role in the distribution of the vesicomyids associated to cold seeps or other reduced environments along the West African margin.

Lumber recovery from young-growth red and white fir in northern California.

Treesearch

W.Y. Pong

1982-01-01

Lumber recovery data from 1,106 logs from 341 young-growth white fir (Abies concolor (Gord. & Glend.) Lindl. ex Hildebr.) and red fir (A. magnifica A. Murr) trees are presented. All logs were processed through a quad-band headsaw. Nominal 2x4's and 2x6's made up over 93 percent of the lumber volume; nearly 70...

Long-term effects of thinning and fertilization on growth of red fir in northeastern California

Treesearch

Jianwei Zhang; William W. Oliver; Robert F. Powers

2005-01-01

To determine the impact of fertilization and thinning on red fir (Abies magnifica) stand growth and development, we established an experiment in a 60-year-old stand using a 2x3 factorial design with nitrogen fertilized and non-fertilized treatments and three stocking levels. Plots were established in 1976 and were measured every 5 years for 26...

Stand structure and growth of Abies magnifica responded to five thinning levels in northeastern California, USA

Treesearch

Jianwei Zhang; William W. Oliver

2006-01-01

A 60-year old red fir stand with 23,950 stems per ha was thinned to five stand densities. Thinning occurred in 1972, 1976, and 1980. Height, DBH, and crown characteristics were measured seven times at four- to seven-year intervals from 1972 to 2002. Tree rings were measured retrospectively to determine growth of individual years. Periodic annual increment (PAI) was...

Mediterranean climate effects. II. Conifer growth phenology across a Sierra Nevada ecotone.

PubMed

Royce, E B; Barbour, M G

2001-05-01

Growth and xylem water potential of the lower elevation conifers Pinus jeffreyi and Abies concolor and the higher elevation Pinus monticola and Abies magnifica were monitored in their montane Mediterranean habitat of the southernmost Sierra Nevada mountains of California. Measurements were made across the ecotone between the midmontane and upper montane forests and through light and heavy snowfall years.Radial stem growth, averaging ∼1.5 mm/yr, started 2 wk after snow melt, providing that maximum air temperatures had reached 21°C, and ended when predawn water potentials fell rapidly at the onset of the summer drought. Leader growth started on or after a fixed date, providing that minimum air temperatures were above -4°C for Pinus species or +2.5°C for Abies species. The cue for leader growth was inferred to be photoperiodic. Leader growth ended when either a determinate internode length of ∼1 mm was reached or predawn water potentials fell rapidly. Abies magnifica grew more rapidly than the low-elevation species, but had a shorter growth period; its annual leader growth, as a consequence, was only 35 mm/yr vs. 50 mm/yr for the low-elevation species. Needle growth was similarly determinate in the absence of early drought. This growth phenology contributes to determining species distribution across the ecotone.

Protective and antioxidant properties of wasp (Vespa magnifica) honeycomb extract: a potential inhibitor against acidified ethanol-induced gastric lesions.

PubMed

Xu, Xue-qing; Yu, Le; Liu, Shu-wen

2011-06-01

To examine the protective effects of wasp (Vespa magnifica) honeycomb extract (WCE) against gastric lesions in rats induced by 60% acidified ethanol, and evaluate its capacity to suppress oxidative stress in the gastric tissue. Wistar rats were subjected to intragastric administration of 60% acidified ethanol to induce gastric lesions following an 8-day oral pretreatment with WCE at 0, 25, 100 and 150 mg/kg or with saline. The levels of 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging, myeloperoxidase (MPO) activity and total antioxidant capacity in the gastric tissues were determined. Oral administration of 25, 100 and 150 mg/kg WCE prior to 60% acidified ethanol administration significantly inhibited the formation of gastric lesions (with a reduction by 44.2%-87.1%), decreased the mucosal MPO activity (by 16.4%-56.6%) and increased the total antioxidant capacity of the gastric tissue (by 0.5, 1.47 and 1.83 folds, respectively) in a dose-dependent manner. At a high concentration (above 1 mg/ml), WCE also exhibited a stronger DPPH radical scavenging activity than butylated hydroxytoluene (BHT). The ethanol extract of wasp honeycombs can suppress the formation of acidified ethanol-induced gastric lesions by reducing free radical oxidation and neutrophils infiltration in the gastric tissue in rats.

Leaching of Copper Ore by Thiobacillus Ferrooxidans.

ERIC Educational Resources Information Center

Lennox, John; Biaha, Thomas

1991-01-01

A quantitative laboratory exercise based upon the procedures copper manufacturers employ to increase copper production is described. The role of chemoautotrophic microorganisms in biogeologic process is emphasized. Safety considerations when working with bacteria are included. (KR)

Immunochemical localization of ribulose-1,5-bisphosphate carboxylase in the symbiont-containing gills of Solemya velum (Bivalvia: Mollusca).

PubMed

Cavanaugh, C M; Abbott, M S; Veenhuis, M

1988-10-01

The distribution of the Calvin cycle enzyme ribulose-1,5-bisphosphate carboxylase (RbuP(2)Case; EC 4.1.1.39) was examined by using two immunological methods in tissues of Solemya velum, an Atlantic coast bivalve containing putative chemoautotrophic symbionts. Antibodies elicited by the purified large subunit of RbuP(2)Case from tobacco (Nicotiana tabacum) cross-reacted on immunoblots with a protein of similar molecular mass occurring in extracts of the symbiont-containing gill tissue of S. velum. No cross-reactivity was detected in symbiont-free tissue extracts. The antiserum also cross-reacted in immunoblots with proteins of Thiobacillus neapolitanus, a free-living sulfuroxidizing chemoautotroph whose RbuP(2)Case has been well characterized. In protein A-gold immunoelectron microscopy studies, this antiserum consistently labeled the symbionts but not surrounding host gill tissue, indicating that the symbionts are responsible for the RbuP(2)Case activity.

Surface and mid-water sources of organic carbon by photoautotrophic and chemoautotrophic production in the Black Sea

NASA Astrophysics Data System (ADS)

Yılmaz, Ayşen; Çoban-Yıldız, Yeşim; Telli-Karakoç, Fatma; Bologa, Alexandru

2006-08-01

The multilayered surface waters of the Black Sea contain aerobic, suboxic and anoxic layers that support both photoautotrophic (PP) and chemoautotrophic (ChP) biological production. During the R/V Knorr cruise in May-June 2001, phytoplankton biomass (represented as chlorophyll- a), photoautotrophic and chemoautotrophic production (ChP) rates were determined in the western Black Sea. Integrated chlorophyll- a concentrations in the euphotic zone were as low as 2.2 mg m -2 in the central gyre, while they were as high as 19.9 mg m -2 in the NW shelf region. Integrated photoautotrophic production rates ranged from 112 to 355 mg C m -2 d -1. The lowest values were determined in the central gyre and the highest values were found at the shelf-break station near the Bosphorus, the NW shelf/shelf-break area and in the Sevastopol eddy. Primary production and chlorophyll- a data revealed that post-bloom conditions existed during this sampling period. Bioassay experiments showed that under optimum light conditions, photoautotrophic production was nitrogen-limited. ChP increased in the redox transition zone and coincided with the lower boundary of the fine particle layer. The maximum values were shallower (at σθ=16.25) in the central gyre and deeper (at σθ=16.5) in the shelf-break region near Sakarya Canyon. Integrated ChP rates were 63 and 1930 mg C m -2 d -1, which were equivalent to 30% and 89% of the overall water-column production for the central gyre and Sakarya Canyon regions, respectively.

Morphology of Clapsiella magnifica gen. n., sp. n., a new hypotrichous ciliate with a curious dorsal ciliary pattern.

PubMed

Küppers, Gabriela Cristina

2014-08-01

The present work describes the morphology and infraciliature of a new hypotrichous ciliate, Clapsiella magnifica gen. n., sp. n., found in rewetted soil from a temporal pond in Argentina. It was studied by means of live observation and protargol impregnation. Its main diagnostic features are: Flexible hypotrich measuring 250-320 μm × 70-140 μm in vivo; two macronuclear nodules and 4-6 micronuclei. Single contractile vacuole. Cytoplasm transparent, cortical granules absent. Somatic ciliature composed of a tricorona of cirri, three buccal(?) cirri, 6-9 ventral rows, 3-5 right marginal(?) rows, one left marginal row, and 12-17 transverse cirri. Dorsal pattern rather complicated, with about 14 kineties and kinety fragments, with scattered kinetids among them; 17-28 caudal cirri arranged in three rows on dorsal kineties 1, 3, and 7. Remarkably, dorsal kinetids have two or four basal bodies, bearing a stiff bristle arising from left anterior basal body. Adoral zone composed of 70-92 membranelles, occupying about 40% of body length in protargol preparations; paroral and endoral curved, resembling a cyrtohymenid pattern. The peculiar dorsal ciliary arrangement and the unique combination of other characters require the establishment of a new genus for this new species, which is considered incertae sedis in the Hypotricha but possibly related to the oxytrichids. Copyright © 2014 Elsevier GmbH. All rights reserved.

Environmental controls on chemoautotrophic primary producers at deep-sea vents

NASA Astrophysics Data System (ADS)

Le Bris, Nadine; Mullineaux, Lauren; Sievert, Stefan

2014-05-01

High biomasses and fast growth rates of dominant chemosynthetic species characterize hydrothermal ecosystems, raising the issue of their contribution to energy transfer and carbon cycling in the deep-sea. Addressing this issue, however, needs to account for the temporal instability of hydrothermal systems, both, in terms of biological colonization and habitat conditions. Volcanic eruptions on mid-ocean ridges offer the opportunity to investigate the environmental conditions favoring the successive modes of chemoautotrophic primary production (i.e. free living microbes and symbiotic invertebrates). In that perspective, habitat-scale approaches distinguish from vent field-scale approaches based on fluid composition and provide relevant information on environmental constraints exerted at different stages of colonization focusing on parameters linked with physiological limits and available energy. Investigation of habitat physicochemical properties along a typical successional sequence of recolonization at 9°50'N EPR diffuse-flow vents, between 2006 and 2014, was performed in order to examine potential changes in environmental features associated with chemoautotrophic primary producers, from early microbial colonizers to symbiotic invertebrates. Combined in situ measurements of temperature, pH and hydrogen sulfide were used and their variability documented over a series of assemblages characterizing recolonization stages. The distributions of mature assemblages of dominant invertebrate species associate with substantial differences in habitat conditions, pointing to a strong influence of habitat properties on potential productivity. Among the differences observed, however, the amplitude and rate of environmental fluctuation appear more important than average conditions in the succession, highlighting the role of spatial heterogeneity and temporal dynamics as a control on primary producers. Invertebrate species acting as engineer species are expected to play a primary role in the rate of organic carbon formed over the lifetime of a vent and potentially transferred to adjacent ecosystems.

Autotrophic processes in meromictic Big Soda Lake, Nevada.

USGS Publications Warehouse

Cloern, J.E.; Cole, B.E.; Oremland, R.S.

1983-01-01

Daily rates of oxygenic photosynthesis (OP) by phytoplankton, anoxygenic photosynthesis (AP) by purple sulfur bacteria, and chemoautotrophic productivity (CP = dark CO2 assimilation) were measured once each season. Total daily productivity and the relative importance of each autotrophic process varied with seasonal changes in vertical mixing, light availability, and the biomass of phototrophs. Daily productivity was highest (2830 mg C.m-2) and was dominated by OP in winter when the mixolimnion was isothermal, the biomass of phytoplankton was high, and the biomass of purple sulfur bacteria was low. During the summer-fall period of thermal stratification, phytoplankton biomass decreased, a plate of purple sulfur bacteria formed below the oxycline, and daily rates of dark CO2 assimilation (CP = 390-680 mg C.m-2) exceeded phototrophic productivity (OP + AP = 200-370 mg C.m-2). Total annual productivity was approx 500 g C.m-2, of which 60% was produced by phytoplankton (mostly in winter), 30% by chemoautotrophs (nitrifying and sulfur-oxidizing bacteria), and only 10% by photosynthetic bacteria. -Authors

Nitrification rates in a headwater stream: influences of seasonal variation in C and N supply

Treesearch

Olyssa S. Starry; H. Maurice Valett

2005-01-01

Nitrification, the chemoautotrophic process by which NH4-N is converted to NO,-N, is an integral biogeochemical transformation in stream ecosystems. Previous research has shown that experimental addition of dissolved organic C inhibits rates of nitrification, and that NH4

Post-Drilling Changes in Seabed Landscape and Megabenthos in a Deep-Sea Hydrothermal System, the Iheya North Field, Okinawa Trough

PubMed Central

Nakajima, Ryota; Yamamoto, Hiroyuki; Kawagucci, Shinsuke; Takaya, Yutaro; Nozaki, Tatsuo; Chen, Chong; Fujikura, Katsunori; Miwa, Tetsuya; Takai, Ken

2015-01-01

There has been an increasing interest in seafloor exploitation such as mineral mining in deep-sea hydrothermal fields, but the environmental impact of anthropogenic disturbance to the seafloor is poorly known. In this study, the effect of such anthropogenic disturbance by scientific drilling operations (IODP Expedition 331) on seabed landscape and megafaunal habitation was surveyed for over 3 years using remotely operated vehicle video observation in a deep-sea hydrothermal field, the Iheya North field, in the Okinawa Trough. We focused on observations from a particular drilling site (Site C0014) where the most dynamic change of landscape and megafaunal habitation was observed among the drilling sites of IODP Exp. 331. No visible hydrothermal fluid discharge had been observed at the sedimentary seafloor at Site C0014, where Calyptogena clam colonies were known for more than 10 years, before the drilling event. After drilling commenced, the original Calyptogena colonies were completely buried by the drilling deposits. Several months after the drilling, diffusing high-temperature hydrothermal fluid began to discharge from the sedimentary subseafloor in the area of over 20 m from the drill holes, ‘artificially’ creating a new hydrothermal vent habitat. Widespread microbial mats developed on the seafloor with the diffusing hydrothermal fluids and the galatheid crab Shinkaia crosnieri endemic to vents dominated the new vent community. The previously soft, sedimentary seafloor was hardened probably due to barite/gypsum mineralization or silicification, becoming rough and undulated with many fissures after the drilling operation. Although the effects of the drilling operation on seabed landscape and megafaunal composition are probably confined to an area of maximally 30 m from the drill holes, the newly established hydrothermal vent ecosystem has already lasted 2 years and is like to continue to exist until the fluid discharge ceases and thus the ecosystem in the area has been altered for long-term. PMID:25902075

Post-drilling changes in seabed landscape and megabenthos in a deep-sea hydrothermal system, the Iheya North field, Okinawa Trough.

PubMed

Nakajima, Ryota; Yamamoto, Hiroyuki; Kawagucci, Shinsuke; Takaya, Yutaro; Nozaki, Tatsuo; Chen, Chong; Fujikura, Katsunori; Miwa, Tetsuya; Takai, Ken

2015-01-01

There has been an increasing interest in seafloor exploitation such as mineral mining in deep-sea hydrothermal fields, but the environmental impact of anthropogenic disturbance to the seafloor is poorly known. In this study, the effect of such anthropogenic disturbance by scientific drilling operations (IODP Expedition 331) on seabed landscape and megafaunal habitation was surveyed for over 3 years using remotely operated vehicle video observation in a deep-sea hydrothermal field, the Iheya North field, in the Okinawa Trough. We focused on observations from a particular drilling site (Site C0014) where the most dynamic change of landscape and megafaunal habitation was observed among the drilling sites of IODP Exp. 331. No visible hydrothermal fluid discharge had been observed at the sedimentary seafloor at Site C0014, where Calyptogena clam colonies were known for more than 10 years, before the drilling event. After drilling commenced, the original Calyptogena colonies were completely buried by the drilling deposits. Several months after the drilling, diffusing high-temperature hydrothermal fluid began to discharge from the sedimentary subseafloor in the area of over 20 m from the drill holes, 'artificially' creating a new hydrothermal vent habitat. Widespread microbial mats developed on the seafloor with the diffusing hydrothermal fluids and the galatheid crab Shinkaia crosnieri endemic to vents dominated the new vent community. The previously soft, sedimentary seafloor was hardened probably due to barite/gypsum mineralization or silicification, becoming rough and undulated with many fissures after the drilling operation. Although the effects of the drilling operation on seabed landscape and megafaunal composition are probably confined to an area of maximally 30 m from the drill holes, the newly established hydrothermal vent ecosystem has already lasted 2 years and is like to continue to exist until the fluid discharge ceases and thus the ecosystem in the area has been altered for long-term.

Inhibitory effect of self-generated extracellular dissolved organic carbon on carbon dioxide fixation in sulfur-oxidizing bacteria during a chemoautotrophic cultivation process and its elimination.

PubMed

Wang, Ya-Nan; Tsang, Yiu Fai; Wang, Lei; Fu, Xiaohua; Hu, Jiajun; Li, Huan; Le, Yiquan

2018-03-01

The features of extracellular dissolved organic carbon (EDOC) generation in two typical aerobic sulfur-oxidizing bacteria (Thiobacillus thioparus DSM 505 and Halothiobacillus neapolitanus DSM 15147) and its impact on CO 2 fixation during chemoautotrophic cultivation process were investigated. The results showed that EDOC accumulated in both strains during CO 2 fixation process. Large molecular weight (MW) EDOC derived from cell lysis and decay was dominant during the entire process in DSM 505, whereas small MW EDOC accounted for a large proportion during initial and middle stages of DSM 15147 as its cytoskeleton synthesis rate did not keep up with CO 2 assimilation rate. The self-generated EDOC feedback repressed cbb gene transcription and thus decreased total bacterial cell number and CO 2 fixation yield in both strains, but DSM 505 was more sensitive to this inhibition effect. Moreover, the membrane bioreactor effectively decreased the EDOC/TOC ratio and improved carbon fixation yield of DSM 505. Copyright © 2017 Elsevier Ltd. All rights reserved.

Oxidative phosphorylation in a thermophilic, facultative chemoautotroph, Hydrogenophilus thermoluteolus, living prevalently in geothermal niches.

PubMed

Wakai, Satoshi; Masanari, Misa; Ikeda, Takumi; Yamaguchi, Naho; Ueshima, Saori; Watanabe, Kaori; Nishihara, Hirofumi; Sambongi, Yoshihiro

2013-04-01

Hydrogenophilus is a thermophilic, facultative chemoautotroph, which lives prevalently in high temperature geothermal niches. Despite the environmental distribution, little is known about its oxidative phosphorylation. Here, we show that inverted membrane vesicles derived from Hydrogenophilus thermoluteolus cells autotrophically cultivated with H2 formed a proton gradient on the addition of succinate, dl-lactate, and NADH, and exhibited oxidation activity toward these three organic compounds. These indicate the capability of mixotrophic growth of this bacterium. Biochemical analysis demonstrated that the same vesicles contained an F-type ATP synthase. The F1 sector of the ATP synthase purified from H. thermoluteolus membranes exhibited optimal ATPase activity at 65°C. Transformed Escherichia coli membranes expressing H. thermoluteolus F-type ATP synthase exhibited the same temperature optimum for the ATPase. These findings shed light on H. thermoluteolus oxidative phosphorylation from the aspects of membrane bioenergetics and ATPase biochemistry, which must be fundamental and advantageous in the biogeochemical cycles occurred in the high temperature geothermal niches. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Geological setting of chemosynthetic communities in the Monterey Fan Valley system

USGS Publications Warehouse

Embley, R.W.; Eittreim, S.L.; McHugh, C.H.; Normark, W.R.; Rau, G.H.; Hecker, Barbara; DeBevoise, A.E.; Greene, H. Gary; Ryan, William B. F.; Harrold, C.; Baxter, C.

1990-01-01

Alvin dives and camera tows within the "meander area" of the Monterey and Ascension Fan Valleys have located nine chemosynthetic communities over depths ranging from 3000 to 3600 m over a distance of 55 km. Most of the observed communities consist largely of Calyptogena phaseoliformis, but Solemya (species unknown) and a pogonophoran (genus Polybrachia), have also been identified. The ??13C values (-35.0 to -33.6 per mil) and the presence of APS reductase and ATP sulfurylase in the C. phaseoliformis tissue is consistent with sulfur chemoautotrophy. Two reduced organic matter sources for the H2S are proposed: (1) older beds exposed by the deep erosion (up to 400 m) of the fan valleys and (2) concentrations of anaerobically decomposd organic matter buried in the valley floor. ?? 1990.

Searching for Life Underground: An Analysis of Remote Sensing Observations of a Drill Core from Rio Tinto, Spain for Mineralogical Indications of Biological Activity

NASA Technical Reports Server (NTRS)

Battler, M.; Stoker, C.

2005-01-01

Water is unstable on the surface of Mars, and therefore the Martian surface is not likely to support life. It is possible, however, that liquid water exists beneath the surface of Mars, and thus life might also be found in the subsurface. Subsurface life would most likely be microbial, anaerobic, and chemoautotrophic; these types of biospheres on Earth are rare, and not well understood. Finding water and life are high priorities for Mars exploration, and therefore it is important that we learn to explore the subsurface robotically, by drilling. The Mars Analog Rio Tinto Experiment (MARTE), has searched successfully for a subsurface biosphere at Rio Tinto, Spain [1,2,3,4]. The Rio Tinto study site was selected to search for a subsurface biosphere because the extremely low pH and high concentrations of elements such as iron and copper in the Tinto River suggest the presence of a chemoautotrophic biosphere in the subsurface beneath the river. The Rio Tinto has been recognized as an important mineralogical analog to the Sinus Meridiani site on Mars [5].

Mycorrhizal preference promotes habitat invasion by a native Australian orchid: Microtis media

PubMed Central

De Long, Jonathan R.; Swarts, Nigel D.; Dixon, Kingsley W.; Egerton-Warburton, Louise M.

2013-01-01

Background and Aims Mycorrhizal specialization has been shown to limit recruitment capacity in orchids, but an increasing number of orchids are being documented as invasive or weed-like. The reasons for this proliferation were examined by investigating mycorrhizal fungi and edaphic correlates of Microtis media, an Australian terrestrial orchid that is an aggressive ecosystem and horticultural weed. Methods Molecular identification of fungi cultivated from M. media pelotons, symbiotic in vitro M. media seed germination assays, ex situ fungal baiting of M. media and co-occurring orchid taxa (Caladenia arenicola, Pterostylis sanguinea and Diuris magnifica) and soil physical and chemical analyses were undertaken. Key Results It was found that: (1) M. media associates with a broad taxonomic spectrum of mycobionts including Piriformospora indica, Sebacina vermifera, Tulasnella calospora and Ceratobasidium sp.; (2) germination efficacy of mycorrhizal isolates was greater for fungi isolated from plants in disturbed than in natural habitats; (3) a higher percentage of M. media seeds germinate than D. magnifica, P. sanguinea or C. arenicola seeds when incubated with soil from M. media roots; and (4) M. media–mycorrhizal fungal associations show an unusual breadth of habitat tolerance, especially for soil phosphorus (P) fertility. Conclusions The findings in M. media support the idea that invasive terrestrial orchids may associate with a diversity of fungi that are widespread and common, enhance seed germination in the host plant but not co-occurring orchid species and tolerate a range of habitats. These traits may provide the weedy orchid with a competitive advantage over co-occurring orchid species. If so, invasive orchids are likely to become more broadly distributed and increasingly colonize novel habitats. PMID:23275632

Tri-domain Bifunctional Inhibitor of Metallocarboxypeptidases A and Serine Proteases Isolated from Marine Annelid Sabellastarte magnifica*

PubMed Central

Alonso-del-Rivero, Maday; Trejo, Sebastian A.; Reytor, Mey L.; Rodriguez-de-la-Vega, Monica; Delfin, Julieta; Diaz, Joaquin; González-González, Yamile; Canals, Francesc; Chavez, Maria Angeles; Aviles, Francesc X.

2012-01-01

This study describes a novel bifunctional metallocarboxypeptidase and serine protease inhibitor (SmCI) isolated from the tentacle crown of the annelid Sabellastarte magnifica. SmCI is a 165-residue glycoprotein with a molecular mass of 19.69 kDa (mass spectrometry) and 18 cysteine residues forming nine disulfide bonds. Its cDNA was cloned and sequenced by RT-PCR and nested PCR using degenerated oligonucleotides. Employing this information along with data derived from automatic Edman degradation of peptide fragments, the SmCI sequence was fully characterized, indicating the presence of three bovine pancreatic trypsin inhibitor/Kunitz domains and its high homology with other Kunitz serine protease inhibitors. Enzyme kinetics and structural analyses revealed SmCI to be an inhibitor of human and bovine pancreatic metallocarboxypeptidases of the A-type (but not B-type), with nanomolar Ki values. SmCI is also capable of inhibiting bovine pancreatic trypsin, chymotrypsin, and porcine pancreatic elastase in varying measures. When the inhibitor and its nonglycosylated form (SmCI N23A mutant) were overproduced recombinantly in a Pichia pastoris system, they displayed the dual inhibitory properties of the natural form. Similarly, two bi-domain forms of the inhibitor (recombinant rSmCI D1-D2 and rSmCI D2-D3) as well as its C-terminal domain (rSmCI-D3) were also overproduced. Of these fragments, only the rSmCI D1-D2 bi-domain retained inhibition of metallocarboxypeptidase A but only partially, indicating that the whole tri-domain structure is required for such capability in full. SmCI is the first proteinaceous inhibitor of metallocarboxypeptidases able to act as well on another mechanistic class of proteases (serine-type) and is the first of this kind identified in nature. PMID:22411994

Physiological Ecology of Microorganisms in Subglacial Lake Whillans

PubMed Central

Vick-Majors, Trista J.; Mitchell, Andrew C.; Achberger, Amanda M.; Christner, Brent C.; Dore, John E.; Michaud, Alexander B.; Mikucki, Jill A.; Purcell, Alicia M.; Skidmore, Mark L.; Priscu, John C.

2016-01-01

Subglacial microbial habitats are widespread in glaciated regions of our planet. Some of these environments have been isolated from the atmosphere and from sunlight for many thousands of years. Consequently, ecosystem processes must rely on energy gained from the oxidation of inorganic substrates or detrital organic matter. Subglacial Lake Whillans (SLW) is one of more than 400 subglacial lakes known to exist under the Antarctic ice sheet; however, little is known about microbial physiology and energetics in these systems. When it was sampled through its 800 m thick ice cover in 2013, the SLW water column was shallow (~2 m deep), oxygenated, and possessed sufficient concentrations of C, N, and P substrates to support microbial growth. Here, we use a combination of physiological assays and models to assess the energetics of microbial life in SLW. In general, SLW microorganisms grew slowly in this energy-limited environment. Heterotrophic cellular carbon turnover times, calculated from 3H-thymidine and 3H-leucine incorporation rates, were long (60 to 500 days) while cellular doubling times averaged 196 days. Inferred growth rates (average ~0.006 d−1) obtained from the same incubations were at least an order of magnitude lower than those measured in Antarctic surface lakes and oligotrophic areas of the ocean. Low growth efficiency (8%) indicated that heterotrophic populations in SLW partition a majority of their carbon demand to cellular maintenance rather than growth. Chemoautotrophic CO2-fixation exceeded heterotrophic organic C-demand by a factor of ~1.5. Aerobic respiratory activity associated with heterotrophic and chemoautotrophic metabolism surpassed the estimated supply of oxygen to SLW, implying that microbial activity could deplete the oxygenated waters, resulting in anoxia. We used thermodynamic calculations to examine the biogeochemical and energetic consequences of environmentally imposed switching between aerobic and anaerobic metabolisms in the SLW water column. Heterotrophic metabolisms utilizing acetate and formate as electron donors yielded less energy than chemolithotrophic metabolisms when calculated in terms of energy density, which supports experimental results that showed chemoautotrophic activity in excess of heterotrophic activity. The microbial communities of subglacial lake ecosystems provide important natural laboratories to study the physiological and biogeochemical behavior of microorganisms inhabiting cold, dark environments. PMID:27833599

Alkalilimnicola ehrlichii sp. nov., a novel, arsenite-oxidizing haloalkaliphilic gammaproteobacterium capable of chemoautotrophic or heterotrophic growth with nitrate or oxygen as the electron acceptor

USGS Publications Warehouse

Hoeft, S.E.; Blum, J.S.; Stolz, J.F.; Tabita, F.R.; Witte, B.; King, G.M.; Santini, J.M.; Oremland, R.S.

2007-01-01

A facultative chemoautotrophic bacterium, strain MLHE-1T, was isolated from Mono Lake, an alkaline hypersaline soda lake in California, USA. Cells of strain MLHE-1T were Gram-negative, short motile rods that grew with inorganic electron donors (arsenite, hydrogen, sulfide or thiosulfate) coupled with the reduction of nitrate to nitrite. No aerobic growth was attained with arsenite or sulfide, but hydrogen sustained both aerobic and anaerobic growth. No growth occurred when nitrite or nitrous oxide was substituted for nitrate. Heterotrophic growth was observed under aerobic and anaerobic (nitrate) conditions. Cells of strain MLHE-1T could oxidize but not grow on CO, while CH4 neither supported growth nor was it oxidized. When grown chemoautotrophically, strain MLHE-1T assimilated inorganic carbon via the Calvin-Benson-Bassham reductive pentose phosphate pathway, with the activity of ribulose 1,5-bisphosphate carboxylase (RuBisCO) functioning optimally at 0.1 M NaCl and at pH 7.3. Strain MLHE-1T grew over broad ranges of pH (7.3-10.0; optimum, 9.3), salinity (115-190 g l-1; optimum 30 g l-1) and temperature (113-40 ??C; optimum, 30 ??C). Phylogenetic analysis of 16S rRNA gene sequences placed strain MLHE-1T in the class Gammaproteobacteria (family Ectothiorhodospiraceae) and most closely related to Alkalispirillum mobile (98.5%) and Alkalilimnicola halodurans (98.6%), although none of these three haloalkaliphilic micro-organisms were capable of photoautotrophic growth and only strain MLHE-1T was able to oxidize As(III). On the basis of physiological characteristics and DNA-DNA hybridization data, it is suggested that strain MLHE-1T represents a novel species within the genus Alkalilimnicola for which the name Alkalilimnicola ehrlichii is proposed. The type strain is MLHE-1T (=DSM 17681T =ATCC BAA-1101T). Aspects of the annotated full genome of Alkalilimnicola ehrlichii are discussed in the light of its physiology. ?? 2007 IUMS.

Newly discovered hydrothermal system on the Alarcón Rise, Mexico

NASA Astrophysics Data System (ADS)

Paduan, J. B.; Clague, D. A.; Caress, D. W.; Lundsten, L.; Martin, J. F.; Nieves-Cardoso, C.

2012-12-01

The Alarcón Rise lies at the mouth of the Gulf of California, and is the last segment of the East Pacific Rise before the plate boundary redirects into the gulf. As part of MBARI's expedition to the gulf in 2012, the neovolcanic zone of the entire ridge segment was mapped by MBARI's mapping AUV. 110 potential hydrothermal chimneys were identified in the new high resolution maps, and 70 were visited with the ROV Doc Ricketts, after having been sought in vain without the maps on an expedition in 2003. Two active vent fields were found, and have been named Meyibó and Ja sít from local native languages. They lie 2.5km apart at ~2300m depth, and are associated with a large, young sheet flow 1/3 of the way along the ridge from the south, on the most inflated part of the ridge. The southern field, Meyibó, contains 14 active chimneys (confirmed with ROV observations) nestled in grabens of several highly fractured cones surrounded by the sheet flow, and generally aligned with its discontinuous, 8km-long fissure system. The northern field, Ja sít, is a broad cluster of 8 active chimneys (also confirmed) rising above the sheet flow's channel system, more than 150m from the fissure. The chimneys stand as tall as 18 m. The most vigorous vent "black smoke" (mineral-rich fluid) >300°C and others are bathed in "white smoke". The active chimneys are populated with bacterial mat and dense clumps of Riftia pachyptila with tubes as long as 1.5m. Abundant limpets, Bythograea thermydron and galatheid crabs, and the pink vent fish Thermarces cerberus were on and near the giant tube worms. Alvinellid worms were observed at 2 chimneys. Some cracks in nearby lava flows vented clear fluid and were populated with tubeworms or Calyptogena magnifica clams. Several chimneys exhibited signs of waning activity: dead tubeworms were still attached and only a minor portion of the edifice supported bacterial mat and live tubeworms. Inactive chimneys are more numerous (48 were confirmed with ROV observations; 40 more were not visited but are presumed inactive, as turbid bottom waters were only observed in the vicinity of the active vents). Most are almost 10km NE of the Ja sít active field in a ridge-parallel array stretching 2.3km. These were deeper (to 2392m) and associated with older flows. Some had only recently ceased venting, as clam shell fragments and relatively fragile vent orifices were still present. Inactive chimneys are also intermingled with the active chimneys. Some of the recovered samples have abundant chalcopyrite, but most are predominantly zinc and iron sulfide. Inactive chimneys stand tall in the AUV maps but as they are no longer venting, would not be detected by traditional water-column surveys. Elsewhere, however, sulfide-bearing sediments were also recovered, evidence of prior hydrothermal activity that would not be detected in the AUV maps. Features that could be mistaken for sulfide chimneys also appear in the maps, but morphology distinguishes them as lava pillars along margins of collapsed flows, fault blocks, pressure ridges, or steep summits of pillow mounds.

Bacteria and Acidic Drainage from Coal Refuse: Inhibition by Sodium Lauryl Sulfate and Sodium Benzoate

PubMed Central

Dugan, Patrick R.; Apel, William A.

1983-01-01

The application of an aqueous solution of sodium lauryl sulfate and sodium benzoate to the surface of high-sulfur coal refuse resulted in the inhibition of iron-and sulfur-oxidizing chemoautotrophic bacteria and in the decrease of acidic drainage from the refuse, suggesting that acid drainage can be abated in the field by inhibiting iron- and sulfur-oxidizing bacteria. PMID:16346347

Evolutionary and geologic consequences of organic carbon fixing in the primitive anoxic ocean

NASA Astrophysics Data System (ADS)

Berry, W. B. N.; Wilde, P.

1983-03-01

Steps leading to development of the modern photic-based marine food web are postulated as the result of modifications of the environment, enhanced by the activity of Archean sulfur chemoautotrophs. Such organisms (Anoxium) evolved in an anoxic ocean prior to 3.9 × 109 yr ago at Archean analogs of modern oceanic hydrothermal vents. At this time geothermal energy was more readily available to organisms than photic energy, given atmospheric conditions at the surface similar to Venus, where intensity is low and only middle and red visible wavelengths penetrate the cloudy CO2-rich atmosphere. Competition for the reduced sulfur developed due to oxidation and loss of sulfur to sediments. Consequently, evolutionary advantage shifted to Anoxium isolates that could use alternate energy sources such as light to supplement the diminished supplies of reduced sulfur. Initially, photo-sulfur organisms evolved similar to modern purple bacteria that absorb in the red visible spectra. Subsequent carbon fixing and oxidation improved both the quantity and range of light reaching the ocean surface. This permitted absorption in the blue visible range so that water splitting was now feasible, releasing free oxygen and accelerating oxidation. Eventually, reducing environments became restricted, completing the shift in the principal marine carbon-fixing activity from anoxic chemoautotrophic to aerobic photosynthetic organisms.

Nutritional associations among fauna at hydrocarbon seep communities in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Macavoy, S. E.; Fisher, C. R.; Carney, R. S.; Macko, S. A.

2004-05-01

The Gulf of Mexico supports dense aggregations of megafauna associated with hydrocarbon seeps on the Louisiana Slope. The visually dominant megafauna at the seeps, mussels and tubeworms, derive their nutrition from symbiotic relationships with sulfide or methane oxidizing bacteria. The structure of the tubeworm aggregations provide biogenic habitat for numerous other species of heterotrophic animals. Carbon, nitrogen and sulfur stable isotope analyses of heterotrophic fauna collected with tubeworm aggregations in the Green Canyon Lease area (GC 185) indicate that most of these species derive the bulk of their nutrition from chemoautotrophic sources. The isotope analyses also indicates that although two species may be deriving significant nutritional input from the bivalves, none of the species analyzed are feeding directly on the tubeworms. Grazing gastropods and deposit feeding sipuncluids were used to estimate the isotopic value of the free-living chemoautotrophic bacteria associated with the tubeworms (d13C -32 to -20%; d15N 0 to 7%; d34S -14 to -1 %). The use of tissue d34S analyses in conjunction with tissue d13C and d15N led to several insights into the trophic biology of the communities that would not have been evident from tissue stable C and N analyses alone.

Arsenic, Anaerobes, and Autotrophy.

NASA Astrophysics Data System (ADS)

Oremland, R. S.

2008-12-01

That microbes have resistance to the toxic arsenic oxyanions arsenite [As(III)] and arsenate [As(V)] has been recognized for some time. More recently it was shown that certain prokaryotes can demonstrate As- dependent growth by conserving the energy gained from the aerobic oxidation of As(III) to As(V), or from the reduction of As(V) to As(III) under anaerobic conditions. During the course of our field studies of two alkaline, hypersaline soda lakes (Mono Lake and Searles Lake, CA) we have discovered several new anaerobic chemo- and photo-autotrophic bacteria that can center their energy gain around the redox reactions between As(III) and As(V). Alkalilimnicola ehrlichii, isolated from the water column of Mono Lake is a nitrate-respiring, As(III)-oxidizing chemoautotroph of the gamma-proteobacteria that has a highly flexible metabolism. It can function either as a facultative anaerobe or as a chemo-autotroph, or as a heterotroph (Hoeft et al., 2007). In contrast, strain MLMS-1 of the delta-proteobacteria was also isolated from Mono Lake, but to date is the first example of an obligate As(V)-respirer that is also an obligate chemo-autotroph, gaining its energy via the oxidation of sulfide to sulfate (Hoeft et al., 2004). Strain SLAS-1, isolated from salt-saturated Searles Lake is a member of the Halananerobiales, and can either grow as a heterotroph (lactate e-donor) or chemo- autotroph (sulfide e-donor) while respiring As(V). The fact that it can achieve this feat at salt-saturation (~ 340 g/L) makes it a true extremophile (Oremland et. al., 2005). Finally, strain PHS-1 isolated from a hot spring on Paoha island in Mono Lake is the first example of a photosynthetic bacterium of the gamma- proteobacteria able to link its growth to As(III)-dependent anoxygenic photosynthesis (Kulp et al., 2008). These novel microbes give us new insights into the evolution of arsenic-based metabolism and their role in the biogeochemical cycling of this toxic element. Hoeft, S.E., et al. 2007. Int. J. Syst. Evol. Microbiol. 57: 514 - 512. Hoeft, S.E, et al. 2004. Appl. Environ. Microbiol. 70: 2741 - 2747. Oremland, R.S., et al. 2005. Science 308: 1305 - 1308. Kulp, T.R. et al. 2008. Science 321: 967 - 970.

The Arnon-Buchanan cycle: a retrospective, 1966-2016.

PubMed

Buchanan, Bob B; Sirevåg, Reidun; Fuchs, Georg; Ivanovsky, Ruslan N; Igarashi, Yasuo; Ishii, Masaharu; Tabita, F Robert; Berg, Ivan A

2017-11-01

For the first decade following its description in 1954, the Calvin-Benson cycle was considered the sole pathway of autotrophic CO 2 assimilation. In the early 1960s, experiments with fermentative bacteria uncovered reactions that challenged this concept. Ferredoxin was found to donate electrons directly for the reductive fixation of CO 2 into alpha-keto acids via reactions considered irreversible. Thus, pyruvate and alpha-ketoglutarate could be synthesized from CO 2 , reduced ferredoxin and acetyl-CoA or succinyl-CoA, respectively. This work opened the door to the discovery that reduced ferredoxin could drive the Krebs citric acid cycle in reverse, converting the pathway from its historical role in carbohydrate breakdown to one fixing CO 2 . Originally uncovered in photosynthetic green sulfur bacteria, the Arnon-Buchanan cycle has since been divorced from light and shown to function in a variety of anaerobic chemoautotrophs. In this retrospective, colleagues who worked on the cycle at its inception in 1966 and those presently working in the field trace its development from a controversial reception to its present-day inclusion in textbooks. This pathway is now well established in major groups of chemoautotrophic bacteria, instead of the Calvin-Benson cycle, and is increasingly referred to as the Arnon-Buchanan cycle. In this retrospective, separate sections have been written by the authors indicated. Bob Buchanan wrote the abstract and the concluding comments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sutter, Markus; Roberts, Evan W.; Gonzalez, Raul C.

Carboxysomes are bacterial microcompartments that enhance carbon fixation by concentrating ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and its substrate CO 2 within a proteinaceous shell. They are found in all cyanobacteria, some purple photoautotrophs and many chemoautotrophic bacteria. Carboxysomes consist of a protein shell that encapsulates several hundred molecules of RuBisCO, and contain carbonic anhydrase and other accessory proteins. Genes coding for carboxysome shell components and the encapsulated proteins are typically found together in an operon. The α-carboxysome operon is embedded in a cluster of additional, conserved genes that are presumably related to its function. In many chemoautotrophs, products of the expanded carboxysomemore » locus include CbbO and CbbQ, a member of the AAA+ domain superfamily. We bioinformatically identified subtypes of CbbQ proteins and show that their genes frequently co-occur with both Form IA and Form II RuBisCO. The α-carboxysome-associated ortholog, CsoCbbQ, from Halothiobacillus neapolitanus forms a hexamer in solution and hydrolyzes ATP. The crystal structure shows that CsoCbbQ is a hexamer of the typical AAA+ domain; the additional C-terminal domain, diagnostic of the CbbQ subfamily, structurally fills the inter-monomer gaps, resulting in a distinctly hexagonal shape. Finally, we show that CsoCbbQ interacts with CsoCbbO and is a component of the carboxysome shell, the first example of ATPase activity associated with a bacterial microcompartment.« less

Anaerobic oxidation of arsenite in Mono Lake water and by a facultative, arsenite-oxidizing chemoautotroph, strain MLHE-1

USGS Publications Warehouse

Oremland, R.S.; Hoeft, S.E.; Santini, J.M.; Bano, N.; Hollibaugh, R.A.; Hollibaugh, J.T.

2002-01-01

Arsenite [As(III)]-enriched anoxic bottom water from Mono Lake, California, produced arsenate [As(V)] during incubation with either nitrate or nitrite. No such oxidation occurred in killed controls or in live samples incubated without added nitrate or nitrite. A small amount of biological As(III) oxidation was observed in samples amended with Fe(III) chelated with nitrolotriacetic acid, although some chemical oxidation was also evident in killed controls. A pure culture, strain MLHE-1, that was capable of growth with As(III) as its electron donor and nitrate as its electron acceptor was isolated in a defined mineral salts medium. Cells were also able to grow in nitrate-mineral salts medium by using H2 or sulfide as their electron donor in lieu of As(III). Arsenite-grown cells demonstrated dark 14CO2 fixation, and PCR was used to indicate the presence of a gene encoding ribulose-1,5-biphosphate carboxylase/oxygenase. Strain MLHE-1 is a facultative chemoautotroph, able to grow with these inorganic electron donors and nitrate as its electron acceptor, but heterotrophic growth on acetate was also observed under both aerobic and anaerobic (nitrate) conditions. Phylogenetic analysis of its 16S ribosomal DNA sequence placed strain MLHE-1 within the haloalkaliphilic Ectothiorhodospira of the ??-Proteobacteria. Arsenite oxidation has never been reported for any members of this subgroup of the Proteobacteria.

Metatranscriptional Response of Chemoautotrophic Ifremeria nautilei Endosymbionts to Differing Sulfur Regimes

PubMed Central

Seston, Sherry L.; Beinart, Roxanne A.; Sarode, Neha; Shockey, Abigail C.; Ranjan, Piyush; Ganesh, Sangita; Girguis, Peter R.; Stewart, Frank J.

2016-01-01

Endosymbioses between animals and chemoautotrophic bacteria are ubiquitous at hydrothermal vents. These environments are distinguished by high physico-chemical variability, yet we know little about how these symbioses respond to environmental fluctuations. We therefore examined how the γ-proteobacterial symbionts of the vent snail Ifremeria nautilei respond to changes in sulfur geochemistry. Via shipboard high-pressure incubations, we subjected snails to 105 μM hydrogen sulfide (LS), 350 μM hydrogen sulfide (HS), 300 μM thiosulfate (TS) and seawater without any added inorganic electron donor (ND). While transcript levels of sulfur oxidation genes were largely consistent across treatments, HS and TS treatments stimulated genes for denitrification, nitrogen assimilation, and CO2 fixation, coincident with previously reported enhanced rates of inorganic carbon incorporation and sulfur oxidation in these treatments. Transcripts for genes mediating oxidative damage were enriched in the ND and LS treatments, potentially due to a reduction in O2 scavenging when electron donors were scarce. Oxidative TCA cycle gene transcripts were also more abundant in ND and LS treatments, suggesting that I. nautilei symbionts may be mixotrophic when inorganic electron donors are limiting. These data reveal the extent to which I. nautilei symbionts respond to changes in sulfur concentration and species, and, interpreted alongside coupled biochemical metabolic rates, identify gene targets whose expression patterns may be predictive of holobiont physiology in environmental samples. PMID:27486438

Two Cases of Acute Kidney Injury Due to Multiple Wasp Stings.

PubMed

Vikrant, Sanjay; Parashar, Anupam

2017-09-01

Acute kidney injury (AKI) is an unusual complication of wasp stings. Treatment of established AKI is largely supportive but the preventive strategies are not well documented. This is a report of 2 human cases that developed AKI after multiple wasp stings (Vespa magnifica). Each patient reached the hospital early in their clinical course and was treated with intravenous hydration and urine alkalization. In both the cases the severity of AKI, morbidity, and duration of hospitalization were reduced. The requirement of dialysis therapy was avoided. We propose early treatment with intravenous hydration, diuretic administration, and urine alkalization in such cases to prevent systemic and renal complications. Copyright © 2017 Wilderness Medical Society. Published by Elsevier Inc. All rights reserved.

A New Deep-Sea Hydrothermal Vent Species of Ostracoda (Crustacea) from the Western Pacific: Implications for Adaptation, Endemism, and Dispersal of Ostracodes in Chemosynthetic Systems.

PubMed

Tanaka, Hayato; Yasuhara, Moriaki

2016-10-01

Deep-sea hydrothermal vent fields are among the most extreme habitats on Earth. Major research interests in these ecosystems have focused on the anomalous macrofauna, which are nourished by chemoautotrophic bacterial endosymbionts. In contrast, the meiofauna is largely overlooked in this chemosynthetic environment. The present study describes a new species, Thomontocypris shimanagai sp. nov. (Crustacea: Ostracoda), which was collected from the surface of colonies of neoverrucid barnacles and paralvinellid worms on the chimneys at the Myojin-sho submarine caldera. This is the first discovery of an ostracode from deep-sea hydrothermal vent environments in the western Pacific region. In addition to the species description, we discuss three aspects: 1) adaptation, 2) endemism, and 3) dispersal strategy of the hydrothermal vent ostracodes. Regarding these aspects, we conclude the following: 1) the new species may feed on sloughed-off tissues, mucus secretions, or fecal pellets of sessile organisms, rather than depend on chemoautotrophic bacteria as symbionts for energy; 2) as has been pointed out by other studies, Thomontocypris does not likely represent a vent-specific genus; however, this new species is considered to be endemic at the species level, as it has not been found outside of the type locality; and 3) this new species may have migrated from adjacent deep-sea chemosynthesis-based habitats, such as hydrothermal vents, with wood falls potentially having acted as stepping stones.

Structural Characterization of a Newly Identified Component of α-Carboxysomes: The AAA+ Domain Protein CsoCbbQ

DOE PAGES

Sutter, Markus; Roberts, Evan W.; Gonzalez, Raul C.; ...

2015-11-05

Carboxysomes are bacterial microcompartments that enhance carbon fixation by concentrating ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and its substrate CO 2 within a proteinaceous shell. They are found in all cyanobacteria, some purple photoautotrophs and many chemoautotrophic bacteria. Carboxysomes consist of a protein shell that encapsulates several hundred molecules of RuBisCO, and contain carbonic anhydrase and other accessory proteins. Genes coding for carboxysome shell components and the encapsulated proteins are typically found together in an operon. The α-carboxysome operon is embedded in a cluster of additional, conserved genes that are presumably related to its function. In many chemoautotrophs, products of the expanded carboxysomemore » locus include CbbO and CbbQ, a member of the AAA+ domain superfamily. We bioinformatically identified subtypes of CbbQ proteins and show that their genes frequently co-occur with both Form IA and Form II RuBisCO. The α-carboxysome-associated ortholog, CsoCbbQ, from Halothiobacillus neapolitanus forms a hexamer in solution and hydrolyzes ATP. The crystal structure shows that CsoCbbQ is a hexamer of the typical AAA+ domain; the additional C-terminal domain, diagnostic of the CbbQ subfamily, structurally fills the inter-monomer gaps, resulting in a distinctly hexagonal shape. Finally, we show that CsoCbbQ interacts with CsoCbbO and is a component of the carboxysome shell, the first example of ATPase activity associated with a bacterial microcompartment.« less

Acquisition of a Novel Sulfur-Oxidizing Symbiont in the Gutless Marine Worm Inanidrilus exumae

PubMed Central

2018-01-01

ABSTRACT Gutless phallodrilines are marine annelid worms without a mouth or gut, which live in an obligate association with multiple bacterial endosymbionts that supply them with nutrition. In this study, we discovered an unusual symbiont community in the gutless phallodriline Inanidrilus exumae that differs markedly from the microbiomes of all 22 of the other host species examined. Comparative 16S rRNA gene sequence analysis and fluorescence in situ hybridization revealed that I. exumae harbors cooccurring gamma-, alpha-, and deltaproteobacterial symbionts, while all other known host species harbor gamma- and either alpha- or deltaproteobacterial symbionts. Surprisingly, the primary chemoautotrophic sulfur oxidizer “Candidatus Thiosymbion” that occurs in all other gutless phallodriline hosts does not appear to be present in I. exumae. Instead, I. exumae harbors a bacterial endosymbiont that resembles “Ca. Thiosymbion” morphologically and metabolically but originates from a novel lineage within the class Gammaproteobacteria. This endosymbiont, named Gamma 4 symbiont here, had a 16S rRNA gene sequence that differed by at least 7% from those of other free-living and symbiotic bacteria and by 10% from that of “Ca. Thiosymbion.” Sulfur globules in the Gamma 4 symbiont cells, as well as the presence of genes characteristic for autotrophy (cbbL) and sulfur oxidation (aprA), indicate that this symbiont is a chemoautotrophic sulfur oxidizer. Our results suggest that a novel lineage of free-living bacteria was able to establish a stable and specific association with I. exumae and appears to have displaced the “Ca. Thiosymbion” symbionts originally associated with these hosts. IMPORTANCE All 22 gutless marine phallodriline species examined to date live in a highly specific association with endosymbiotic, chemoautotrophic sulfur oxidizers called “Ca. Thiosymbion.” These symbionts evolved from a single common ancestor and represent the ancestral trait for this host group. They are transmitted vertically and assumed to be in transition to becoming obligate endosymbionts. It is therefore surprising that despite this ancient, evolutionary relationship between phallodriline hosts and “Ca. Thiosymbion,” these symbionts are apparently no longer present in Inanidrilus exumae. They appear to have been displaced by a novel lineage of sulfur-oxidizing bacteria only very distantly related to “Ca. Thiosymbion.” Thus, this study highlights the remarkable plasticity of both animals and bacteria in establishing beneficial associations: the phallodriline hosts were able to acquire and maintain symbionts from two very different lineages of bacteria, while sulfur-oxidizing bacteria from two very distantly related lineages were able to independently establish symbiotic relationships with phallodriline hosts. PMID:29330187

Lebetimonas natsushimae sp. nov., a novel strictly anaerobic, moderately thermophilic chemoautotroph isolated from a deep-sea hydrothermal vent polychaete nest in the Mid-Okinawa Trough.

PubMed

Nagata, Ryousuke; Takaki, Yoshihiro; Tame, Akihiro; Nunoura, Takuro; Muto, Hisashi; Mino, Sayaka; Sawayama, Shigeki; Takai, Ken; Nakagawa, Satoshi

2017-09-01

A moderately thermophilic, strictly anaerobic, chemoautotrophic bacterium, designated strain HS1857 T , was isolated from a deep-sea hydrothermal vent at the Noho site in the Mid-Okinawa Trough. Strain HS1857 T grew between 35 and 63°C (optimum 55°C), in the presence of 10-55gl -1 NaCl (optimum 25gl -1 ), and pH 5.5-7.1 (optimum 6.4). Growth occurred with molecular hydrogen as the electron donor and elemental sulfur, nitrate, or selenate as the electron acceptors. Formate could serve as an alternative electron donor with nitrate as an electron acceptor. During growth with nitrate as the electron acceptor, strain HS1857 T produced ammonium and formed a biofilm. CO 2 was utilized as the sole carbon source. The G+C content of the genomic DNA was 33.2mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain HS1857 T is a member of the order Nautiliales, showing a sequence similarity of 95.0% with Lebetimonas acidiphila Pd55 T . The fatty acid composition was similar to that of L. acidiphila, which was dominated by C 18:0 (47.0%) and C 18:1 (23.7%). Based on the genomic, chemotaxonomic, phenotypic characteristics, the name Lebetimonas natsushimae sp. nov., is proposed. The type strain is HS1857 T (=NBRC 112478 T =DSM 104102 T ). Copyright © 2017 Elsevier GmbH. All rights reserved.

Cold Seep Epifaunal Communities on the Hikurangi Margin, New Zealand: Composition, Succession, and Vulnerability to Human Activities

PubMed Central

Bowden, David A.; Rowden, Ashley A.; Thurber, Andrew R.; Baco, Amy R.; Levin, Lisa A.; Smith, Craig R.

2013-01-01

Cold seep communities with distinctive chemoautotrophic fauna occur where hydrocarbon-rich fluids escape from the seabed. We describe community composition, population densities, spatial extent, and within-region variability of epifaunal communities at methane-rich cold seep sites on the Hikurangi Margin, New Zealand. Using data from towed camera transects, we match observations to information about the probable life-history characteristics of the principal fauna to develop a hypothetical succession sequence for the Hikurangi seep communities, from the onset of fluid flux to senescence. New Zealand seep communities exhibit taxa characteristic of seeps in other regions, including predominance of large siboglinid tubeworms, vesicomyid clams, and bathymodiolin mussels. Some aspects appear to be novel; however, particularly the association of dense populations of ampharetid polychaetes with high-sulphide, high-methane flux, soft-sediment microhabitats. The common occurrence of these ampharetids suggests they play a role in conditioning sulphide-rich sediments at the sediment-water interface, thus facilitating settlement of clam and tubeworm taxa which dominate space during later successional stages. The seep sites are subject to disturbance from bottom trawling at present and potentially from gas hydrate extraction in future. The likely life-history characteristics of the dominant megafauna suggest that while ampharetids, clams, and mussels exploit ephemeral resources through rapid growth and reproduction, lamellibrachid tubeworm populations may persist potentially for centuries. The potential consequences of gas hydrate extraction cannot be fully assessed until extraction methods and target localities are defined but any long-term modification of fluid flow to seep sites would have consequences for all chemoautotrophic fauna. PMID:24204691

Cold seep epifaunal communities on the Hikurangi margin, New Zealand: composition, succession, and vulnerability to human activities.

PubMed

Bowden, David A; Rowden, Ashley A; Thurber, Andrew R; Baco, Amy R; Levin, Lisa A; Smith, Craig R

2013-01-01

Cold seep communities with distinctive chemoautotrophic fauna occur where hydrocarbon-rich fluids escape from the seabed. We describe community composition, population densities, spatial extent, and within-region variability of epifaunal communities at methane-rich cold seep sites on the Hikurangi Margin, New Zealand. Using data from towed camera transects, we match observations to information about the probable life-history characteristics of the principal fauna to develop a hypothetical succession sequence for the Hikurangi seep communities, from the onset of fluid flux to senescence. New Zealand seep communities exhibit taxa characteristic of seeps in other regions, including predominance of large siboglinid tubeworms, vesicomyid clams, and bathymodiolin mussels. Some aspects appear to be novel; however, particularly the association of dense populations of ampharetid polychaetes with high-sulphide, high-methane flux, soft-sediment microhabitats. The common occurrence of these ampharetids suggests they play a role in conditioning sulphide-rich sediments at the sediment-water interface, thus facilitating settlement of clam and tubeworm taxa which dominate space during later successional stages. The seep sites are subject to disturbance from bottom trawling at present and potentially from gas hydrate extraction in future. The likely life-history characteristics of the dominant megafauna suggest that while ampharetids, clams, and mussels exploit ephemeral resources through rapid growth and reproduction, lamellibrachid tubeworm populations may persist potentially for centuries. The potential consequences of gas hydrate extraction cannot be fully assessed until extraction methods and target localities are defined but any long-term modification of fluid flow to seep sites would have consequences for all chemoautotrophic fauna.

Microbial carbon metabolism associated with electrogenic sulphur oxidation in coastal sediments.

PubMed

Vasquez-Cardenas, Diana; van de Vossenberg, Jack; Polerecky, Lubos; Malkin, Sairah Y; Schauer, Regina; Hidalgo-Martinez, Silvia; Confurius, Veronique; Middelburg, Jack J; Meysman, Filip J R; Boschker, Henricus T S

2015-09-01

Recently, a novel electrogenic type of sulphur oxidation was documented in marine sediments, whereby filamentous cable bacteria (Desulfobulbaceae) are mediating electron transport over cm-scale distances. These cable bacteria are capable of developing an extensive network within days, implying a highly efficient carbon acquisition strategy. Presently, the carbon metabolism of cable bacteria is unknown, and hence we adopted a multidisciplinary approach to study the carbon substrate utilization of both cable bacteria and associated microbial community in sediment incubations. Fluorescence in situ hybridization showed rapid downward growth of cable bacteria, concomitant with high rates of electrogenic sulphur oxidation, as quantified by microelectrode profiling. We studied heterotrophy and autotrophy by following (13)C-propionate and -bicarbonate incorporation into bacterial fatty acids. This biomarker analysis showed that propionate uptake was limited to fatty acid signatures typical for the genus Desulfobulbus. The nanoscale secondary ion mass spectrometry analysis confirmed heterotrophic rather than autotrophic growth of cable bacteria. Still, high bicarbonate uptake was observed in concert with the development of cable bacteria. Clone libraries of 16S complementary DNA showed numerous sequences associated to chemoautotrophic sulphur-oxidizing Epsilon- and Gammaproteobacteria, whereas (13)C-bicarbonate biomarker labelling suggested that these sulphur-oxidizing bacteria were active far below the oxygen penetration. A targeted manipulation experiment demonstrated that chemoautotrophic carbon fixation was tightly linked to the heterotrophic activity of the cable bacteria down to cm depth. Overall, the results suggest that electrogenic sulphur oxidation is performed by a microbial consortium, consisting of chemoorganotrophic cable bacteria and chemolithoautotrophic Epsilon- and Gammaproteobacteria. The metabolic linkage between these two groups is presently unknown and needs further study.

Oxidoreductase mimic activity of natural pyrrhotite

NASA Astrophysics Data System (ADS)

Ibáñez de Aldecoa, A. L.; Velasco, F.; Menor-Salván, C.

2012-09-01

The theory of the chemo-autotrophic origin of life, also called the "iron-sulfur world hypothesis", proposes that the system FeS/FeS2 present in the primitive Earth crust gave the reductive power necessary to conduct the first protometabolic redox reactions. Some experimental studies demonstrated the redox activity of the FeS/SH2 system, but none of them used natural FeS. Here, we show that the iron sulfide mineral pyrrhotite is able to mimic the redox activity of the enzyme lactate dehydrogenase, which reversibly reduces the pyruvate in lactate, under prebiotic conditions with pyrite formation.

Mars Analog Research and Technology Experiment (MARTE): A Simulated Mars Drilling Mission to Search for Subsurface Life at the Rio Tinto, Spain

NASA Technical Reports Server (NTRS)

Stoker, Carol; Lemke, Larry; Mandell, Humboldt; McKay, David; George, Jeffrey; Gomez-Alvera, Javier; Amils, Ricardo; Stevens, Todd; Miller, David

2003-01-01

The MARTE (Mars Astrobiology Research and Technology Experiment) project was selected by the new NASA ASTEP program, which supports field experiments having an equal emphasis on Astrobiology science and technology development relevant to future Astrobiology missions. MARTE will search for a hypothesized subsurface anaerobic chemoautotrophic biosphere in the region of the Tinto River in southwestern Spain while also demonstrating technology needed to search for a subsurface biosphere on Mars. The experiment is informed by the strategy for searching for life on Mars.

Thinking of biology: asteroid impacts, microbes, and the cooling of the atmosphere

NASA Technical Reports Server (NTRS)

Oberbeck, V. R.; Mancinelli, R. L.

1994-01-01

The authors examine the cooling of the Earth's surface from 3.75 to 1 billion years ago. Three effects of the bombardment of Earth by asteroids and comets that may have delayed surface cooling include time to form continents, volatilization of carbonate rocks which released carbon dioxide into the atmosphere, and inability of microbes to inhabit land masses during large impact events. Continental microbes may have helped reduce high temperatures from 3.75 to 3.5 billion years ago. If so, the evolutionary sequence of microbes is proposed to be anaerobic heterotrophs, chemoautotrophs, and then photoautotrophs.

Culture-Independent Identification of Manganese-Oxidizing Genes from Deep-Sea Hydrothermal Vent Chemoautotrophic Ferromanganese Microbial Communities Using a Metagenomic Approach

NASA Astrophysics Data System (ADS)

Davis, R.; Tebo, B. M.

2013-12-01

Microbial activity has long been recognized as being important to the fate of manganese (Mn) in hydrothermal systems, yet we know very little about the organisms that catalyze Mn oxidation, the mechanisms by which Mn is oxidized or the physiological function that Mn oxidation serves in these hydrothermal systems. Hydrothermal vents with thick ferromanganese microbial mats and Mn oxide-coated rocks observed throughout the Pacific Ring of Fire are ideal models to study the mechanisms of microbial Mn oxidation, as well as primary productivity in these metal-cycling ecosystems. We sampled ferromanganese microbial mats from Vai Lili Vent Field (Tmax=43°C) located on the Eastern Lau Spreading Center and Mn oxide-encrusted rhyolytic pumice (4°C) from Niua South Seamount on the Tonga Volcanic Arc. Metagenomic libraries were constructed and assembled from these samples and key genes known to be involved in Mn oxidation and carbon fixation pathways were identified in the reconstructed genomes. The Vai Lili metagenome assembled to form 121,157 contiguous sequences (contigs) greater than 1000bp in length, with an N50 of 8,261bp and a total metagenome size of 593 Mbp. Contigs were binned using an emergent self-organizing map of tetranucleotide frequencies. Putative homologs of the multicopper Mn-oxidase MnxG were found in the metagenome that were related to both the Pseudomonas-like and Bacillus-like forms of the enzyme. The bins containing the Pseudomonas-like mnxG genes are most closely related to uncultured Deltaproteobacteria and Chloroflexi. The Deltaproteobacteria bin appears to be an obligate anaerobe with possible chemoautotrophic metabolisms, while the Chloroflexi appears to be a heterotrophic organism. The metagenome from the Mn-stained pumice was assembled into 122,092 contigs greater than 1000bp in length with an N50 of 7635 and a metagenome size of 385 Mbp. Both forms of mnxG genes are present in this metagenome as well as the genes encoding the putative Mn oxidases McoA and MopA. The greater diversity of Mn oxidase pathways in this metagenome suggests a more diverse Mn oxidizing microbial community in the cold pumice sample. Key enzymes for four of the six known carbon fixation pathways (the Calvin Cycle, the reductive TCA cycle, the Wood-Ljungdahl pathway, and the 3-hydroxypropionate/4-hydroxybutyrate Cycle) were also identified in both samples indicating primary production occurs via a diverse community of carbon fixing organisms. Together, these samples contain active, diverse populations of Mn oxidizing bacteria living in association with microbial communities supported by chemoautotrophic carbon fixation.

Evaluation of nutrient and energy sources of the deepest known serpentinite-hosted ecosystem using stable carbon, nitrogen, and sulfur isotopes.

PubMed

Onishi, Yuji; Yamanaka, Toshiro; Okumura, Tomoyo; Kawagucci, Shinsuke; Watanabe, Hiromi Kayama; Ohara, Yasuhiko

2018-01-01

The Shinkai Seep Field (SSF) in the southern Mariana forearc discovered in 2010 is the deepest (~5,700 m in depth) known serpentinite-hosted ecosystem dominated by a vesicomyid clam, Calyptogena (Abyssogena) mariana. The pioneering study presumed that the animal communities are primary sustained by reducing fluid originated from the serpentinization of mantle peridotite. For understanding the nutrient and energy sources for the SSF community, this study conducted four expeditions to the SSF and collected additional animal samples such as polychaetes and crustaceans as well as sediments, fragments of chimneys developing on fissures of serpentinized peridotite, seeping fluid on the chimneys, and pore water within the chimneys. Geochemical analyses of seeping fluids on the chimneys and pore water of the chimneys revealed significantly high pH (~10) that suggest subseafloor serpentinization controlling fluid chemistry. Stable isotope systematics (carbon, nitrogen, and sulfur) among animals, inorganic molecules, and environmental organic matter suggest that the SSF animal community mostly relies on the chemosynthetic production while some organisms appear to partly benefit from photosynthetic production despite the great depth of SSF.

Strategy for modeling putative multilevel ecosystems on Europa.

PubMed

Irwin, Louis N; Schulze-Makuch, Dirk

2003-01-01

A general strategy for modeling ecosystems on other worlds is described. Two alternative biospheres beneath the ice surface of Europa are modeled, based on analogous ecosystems on Earth in potentially comparable habitats, with reallocation of biomass quantities consistent with different sources of energy and chemical constituents. The first ecosystem models a benthic biosphere supported by chemoautotrophic producers. The second models two concentrations of biota at the top and bottom of the subsurface water column supported by energy harvested from transmembrane ionic gradients. Calculations indicate the plausibility of both ecosystems, including small macroorganisms at the highest trophic levels, with ionotrophy supporting a larger biomass than chemoautotrophy.

Prebiotic NH3 Formation: Insights from Simulations.

PubMed

Stirling, András; Rozgonyi, Tamás; Krack, Matthias; Bernasconi, Marco

2016-02-15

Simulations of prebiotic NH₃ synthesis from NO₃⁻ and NO₂⁻ on pyrite surfaces under hydrothermal conditions are reported. Ab initio metadynamics calculations have successfully explored the full reaction path which explains earlier experimental observations. We have found that the reaction mechanism can be constructed from stepwise single atom transfers which are compatible with the expected reaction time scales. The roles of the hot-pressurized water and of the pyrite surfaces have been addressed. The mechanistic picture that emerged from the simulations strengthens the theory of chemoautotrophic origin of life by providing plausible reaction pathways for the formation of ammonia within the iron-sulfur-world scenario.

City sewer collectors biocorrosion

NASA Astrophysics Data System (ADS)

Ksiażek, Mariusz

2014-12-01

This paper presents the biocorrosion of city sewer collectors impregnated with special polymer sulphur binders, polymerized sulphur, which is applied as the industrial waste material. The city sewer collectors are settled with a colony of soil bacteria which have corrosive effects on its structure. Chemoautotrophic nitrifying bacteria utilize the residues of halites (carbamide) which migrate in the city sewer collectors, due to the damaged dampproofing of the roadway and produce nitrogen salts. Chemoorganotrophic bacteria utilize the traces of organic substrates and produce a number of organic acids (formic, acetic, propionic, citric, oxalic and other). The activity of microorganisms so enables the origination of primary and secondary salts which affect physical properties of concretes in city sewer collectors unfavourably.

Interrogating the Bioactive Pharmacophore of the Latrunculin Chemotype by Investigating the Metabolites of Two Taxonomically Unrelated Sponges

PubMed Central

Amagata, Taro; Johnson, Tyler A.; Cichewicz, Robert H.; Tenney, Karen; Mooberry, Susan L.; Media, Joseph; Edelstein, Matthew; Valeriote, Frederick A.; Crews, Phillip

2009-01-01

This study involved a campaign to isolate and study additional latrunculin analogs from two taxonomically unrelated sponges, Cacospongia mycofijiensis and Negombata magnifica. A total of 13 latrunculin analogs were obtained by four different ways, reisolation (1–4), our repository (5–6), new derivatives (7–12), and a synthetic analog (7a). The structures of the new metabolites were elucidated based on a combination of comprehensive 1D and 2D NMR analysis, application of DFT calculations, and the preparation of acetonide derivative 7a. The cytotoxicities against both murine and human cancer cell lines observed for 1, 2, 7, 7a, 8, 9, and 12 were significant and the IC50 value range was 0.5–10 μM. Among the cytotoxic derivatives, compound 9 did not exhibit microfilament-disrupting activity at 5 μM. The implications of this observation and the value of further therapeutic study on key latrunculin derivatives are discussed. PMID:18942825

From Mantle to Microbe to Mollusc: How Animal-Microbial Symbioses Influence Carbon and Sulfur Cycling in Hydrothermal Vent Flows.

NASA Astrophysics Data System (ADS)

Girguis, P. R.; Beinart, R.

2014-12-01

Symbioses between animals and chemoautotrophic bacteria dominate many hydrothermal vents. In these associations, symbiotic bacteria harness energy and "fix" carbon from the oxidation of reduced chemicals such as sulfide, methane, and hydrogen that are found in venting fluids. At vents along the Eastern Lau Spreading Center (ELSC) in the South Pacific, snails and mussels with chemoautotrophic symbionts have been shown to harness energy via the oxidation of sulfide. However, partially oxidized sulfur species such as thiosulfate and polysulfides have also been detected in abundance in their habitats. No studies to date have established whether thiosulfate or other partially oxidized sulfur compounds are used by these symbiotic associations, nor have studies constrained the potential role that symbioses might play in sulfur biogeochemical cycles at diffuse vent flows. To address these questions, we used high-pressure, flow through incubations to study three symbiotic molluscs from the ELSC - the snails Alviniconcha and Ifremeria nautilei and the mussel Bathymodiolus brevior - at conditions mimicking those in situ. Via the use of isotopically labeled inorganic carbon, shipboard mass spectrometry and voltammetric microelectrodes, we quantified the production and consumption of different sulfur compounds by each of these symbioses. We established that the uptake and oxidation of either sulfide or thiosulfate could -to varying degrees- support carbon fixation in all three species. Notably, we also observed that some symbioses excreted thiosulfate and polysulfides under sulfidic conditions, suggesting that these symbioses are a source of partially oxidized sulfur species in the environment. We further observed spatial disparity in the carbon fixation rates among the individuals in our incubations that have implications for the variability of productivity in situ.Collectively, these data reveal that thiosulfate can support net autotrophy, and may be an ecologically important energy source for vent symbioses. Furthermore, symbioses-mediated sulfur transformations may influence the ecology of the free-living community by governing the production and consumption of reduced sulfur species in this habitat.

Earth analogs for Martian life - Microbes in evaporites, a new model system for life on Mars

NASA Technical Reports Server (NTRS)

Rothschild, Lynn J.

1990-01-01

It is suggested that 'oases' in which life forms may persist on Mars could occur, by analogy with terrestrial cases, in (1) rocks, as known in endolithic microorganisms, (2) polar ice caps, as seen in snow and ice algae, and (3) volcanic regions, as witnessed in the chemoautotrophs which live in ocean-floor hydrothermal vents. Microorganisms, moreover, have been known to survive in salt crystals, and it has even been shown that organisms can metabolize while encrusted in evaporites. Evaporites which may occur on Mars would be able to attenuate UV light, while remaining more transparent to the 400-700 nm radiation useful in photosynthesis. Suggestions are made for the selection of Martian exobiological investigation sites.

Environmental genomics reveals a single species ecosystem deep within the Earth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chivian, Dylan; Brodie, Eoin L.; Alm, Eric J.

DNA from low biodiversity fracture water collected at 2.8 km depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, comprises>99.9percent of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent lifestyle well suited to long-term isolation from the photosphere deep within Earth?s crust, and offers the first example of a natural ecosystem that appears to havemore » its biological component entirely encoded within a single genome.« less

Surfing the vegetal pole in a small population: extracellular vertical transmission of an 'intracellular' deep-sea clam symbiont.

PubMed

Ikuta, Tetsuro; Igawa, Kanae; Tame, Akihiro; Kuroiwa, Tsuneyoshi; Kuroiwa, Haruko; Aoki, Yui; Takaki, Yoshihiro; Nagai, Yukiko; Ozawa, Genki; Yamamoto, Masahiro; Deguchi, Ryusaku; Fujikura, Katsunori; Maruyama, Tadashi; Yoshida, Takao

2016-05-01

Symbiont transmission is a key event for understanding the processes underlying symbiotic associations and their evolution. However, our understanding of the mechanisms of symbiont transmission remains still fragmentary. The deep-sea clam Calyptogena okutanii harbours obligate sulfur-oxidizing intracellular symbiotic bacteria in the gill epithelial cells. In this study, we determined the localization of their symbiont associating with the spawned eggs, and the population size of the symbiont transmitted via the eggs. We show that the symbionts are located on the outer surface of the egg plasma membrane at the vegetal pole, and that each egg carries approximately 400 symbiont cells, each of which contains close to 10 genomic copies. The very small population size of the symbiont transmitted via the eggs might narrow the bottleneck and increase genetic drift, while polyploidy and its transient extracellular lifestyle might slow the rate of genome reduction. Additionally, the extracellular localization of the symbiont on the egg surface may increase the chance of symbiont exchange. This new type of extracellular transovarial transmission provides insights into complex interactions between the host and symbiont, development of both host and symbiont, as well as the population dynamics underlying genetic drift and genome evolution in microorganisms.

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation

NASA Astrophysics Data System (ADS)

Pachiadaki, Maria G.; Sintes, Eva; Bergauer, Kristin; Brown, Julia M.; Record, Nicholas R.; Swan, Brandon K.; Mathyer, Mary Elizabeth; Hallam, Steven J.; Lopez-Garcia, Purificacion; Takaki, Yoshihiro; Nunoura, Takuro; Woyke, Tanja; Herndl, Gerhard J.; Stepanauskas, Ramunas

2017-11-01

Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean’s interior, but the relevant taxa and energy sources remain enigmatic. We show evidence that nitrite-oxidizing bacteria affiliated with the Nitrospinae phylum are important in dark ocean chemoautotrophy. Single-cell genomics and community metagenomics revealed that Nitrospinae are the most abundant and globally distributed nitrite-oxidizing bacteria in the ocean. Metaproteomics and metatranscriptomics analyses suggest that nitrite oxidation is the main pathway of energy production in Nitrospinae. Microautoradiography, linked with catalyzed reporter deposition fluorescence in situ hybridization, indicated that Nitrospinae fix 15 to 45% of inorganic carbon in the mesopelagic western North Atlantic. Nitrite oxidation may have a greater impact on the carbon cycle than previously assumed.

Effect of zinc and benzalkonium chloride on Nitrosomonas communis and potential nitrification in soil.

PubMed

Frühling, W; Rönnpagel, K; Ahlf, W

2001-10-01

A bacterial contact assay is described which uses a chemoautotrophic microorganism, Nitrosomonas communis (strain Nm2) to evaluate the biological effect of contaminated soils. The effects of two toxicants on the ammonium oxidation activity of the autochthonous microbial population in the soil are compared with inhibition of the same biological response in the new monospecies bioassay. Experiments were performed using soil samples dosed with organic and inorganic contaminants (benzalkonium chloride and zinc) to demonstrate the mode of operation and the sensitivity of the bioassay. The EC50 values of zinc and benzalkonium chloride were calculated to be 171 and 221 mg kg-1 soil, respectively. The toxic response provided by the bioassay can thus predict the effect of soil pollutants on the autochthonous nitrifying bacteria.

Evidence for microbial carbon and sulfur cycling in deeply buried ridge flank basalt

USGS Publications Warehouse

Lever, Mark A.; Rouxel, Olivier; Alt, Jeffrey C.; Shimizu, Nobumichi; Ono, Shuhei; Coggon, Rosalind M.; Shanks, Wayne C.; Lapham, Laura; Elvert, Marcus; Prieto-Mollar, Xavier; Hinrichs, Kai-Uwe; Inagaki, Fumio; Teske, Andreas

2013-01-01

Sediment-covered basalt on the flanks of mid-ocean ridges constitutes most of Earth's oceanic crust, but the composition and metabolic function of its microbial ecosystem are largely unknown. By drilling into 3.5-million-year-old subseafloor basalt, we demonstrated the presence of methane- and sulfur-cycling microbes on the eastern flank of the Juan de Fuca Ridge. Depth horizons with functional genes indicative of methane-cycling and sulfate-reducing microorganisms are enriched in solid-phase sulfur and total organic carbon, host δ13C- and δ34S-isotopic values with a biological imprint, and show clear signs of microbial activity when incubated in the laboratory. Downcore changes in carbon and sulfur cycling show discrete geochemical intervals with chemoautotrophic δ13C signatures locally attenuated by heterotrophic metabolism.

Cutaneous myiasis: a review of the common types of myiasis.

PubMed

Robbins, Kerri; Khachemoune, Amor

2010-10-01

Myiasis is derived from the Greek word, myia, meaning fly. The term was first introduced by Hope in 1840 and refers to the infestation of live human and vertebrate animals with dipterous (two-winged) larvae (maggots) which, at least for a certain period, feed on the host's dead or living tissue, liquid body-substance, or ingested food. Myiasis is the fourth most common travel-associated skin disease and cutaneous myiasis is the most frequently encountered clinical form. Cutaneous myiasis can be divided into three main clinical manifestations: furuncular, creeping (migratory), and wound (traumatic) myiasis. The flies that produce a furuncular myiasis include Dermatobia hominis, Cordylobia anthropophaga, Wohlfahrtia vigil, and the Cuterebra species. Gasterophilus and Hypoderma are two flies that produce a creeping myiasis. Flies that cause wound myiasis include screwworm flies such as Cochliomyia hominivorax and Chrysomya bezziana, and Wohlfahrtia magnifica. This article reviews current literature, provides general descriptions, and discusses life cycles of each species. It also gives treatment techniques and descriptions of each type of illness that results from interaction/infestation. © 2010 The International Society of Dermatology.

Microbial oxidation of elemental selenium in soil slurries and bacterial cultures

USGS Publications Warehouse

Dowdle, P.R.; Oremland, R.S.

1998-01-01

The microbial oxidation of elemental selenium [Se(O)] was studied by employing 75Se(O) as a tracer. Live, oxic soil slurries demonstrated a linear production of mostly Se(IV), with the formation of smaller quantities of Se(VI). Production of both Se(IV) and Se(VI) was inhibited by autoclaving, formalin, antibiotics, azide, and 2,4-dinitrophenol, thereby indicating the involvement of microbes. Oxidation of Se(O) in slurries was enhanced by addition of acetate, glucose, or sulfide, which implied involvement of chemoheterotrophs as well as chemoautotrophic thiobacilli. Cultures of Thiobacillus ASN-1, Leptothrix MnB1, and a heterotrophic soil enrichment all oxidized Se(O) with Se(VI) observed as the major product rather than Se(IV). This indicated that microbial oxidation in soils is partly constrained by the adsorption of Se(IV) onto soil surfaces. Rate constants for unamended soil slurry Se(O) oxidation ranged from 0.0009 to 0.0117 day-1 which were 3-4 orders of magnitude lower than those reported for dissimilatory Se(VI) reduction in organic-rich, anoxic sediments.The microbial oxidation of elemental selenium [Se(0)] was studied by employing 75Se(0) as a tracer. Live, oxic soil slurries demonstrated a linear production of mostly Se(IV), with the formation of smaller quantities of Se(VI). Production of both Se(IV) and Se(VI) was inhibited by autoclaving, formalin, antibiotics, azide, and 2,4-dinitrophenol, thereby indicating the involvement of microbes. Oxidation of Se(O) in slurries was enhanced by addition of acetate, glucose, or sulfide, which implied involvement of chemoheterotrophs as well as chemoautotrophic thiobacilli. Cultures of Thiobacillus ASN-1, Leptothrix MnB1, and a heterotrophic soil enrichment all oxidized Se(O) with Se(VI) observed as the major product rather than Se(IV). This indicated that microbial oxidation in soils is partly constrained by the adsorption of Se(IV) onto soil surfaces. Rate constants for unamended soil slurry Se(O) oxidation ranged from 0.0009 to 0.0117 day-1 which were 3-4 orders of magnitude lower than those reported for dissimilatory Se(VI) reduction in organic-rich, anoxic sediments.

Partial resolution of sources of n-alkanes in the saline portion of the Parachute Creek Member, Green River Formation (Piceance Creek Basin, Colorado)

NASA Technical Reports Server (NTRS)

Collister, J. W.; Lichtfouse, E.; Hieshima, G.; Hayes, J. M.

1994-01-01

Systematic variations in the 13C contents of individual extractable n-alkanes (C16-C29) can be modelled quantitatively and interpreted as indicating contributions from at least five distinct sources. These appear to be cyanobacterial (C16-C18, delta 13C = -37% vs PDB), phytoplanktonic (C16-C23, delta = -32%), chemoautotrophic bacterial (C20-C29, delta = -38%), phytoplanktonic or heterotrophic bacterial (C20-C29, delta = -30%), and vascular plants (C23-C29, delta = -29%). Hydrous pyrolysis of related kerogens yields large quantities of additional n-alkanes with different and much more uniform delta values. The latter materials are apparently derived from the thermolysis of aliphatic biopolymers whose presence in the Green River Oil Shale has been recognized visually.

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation.

PubMed

Pachiadaki, Maria G; Sintes, Eva; Bergauer, Kristin; Brown, Julia M; Record, Nicholas R; Swan, Brandon K; Mathyer, Mary Elizabeth; Hallam, Steven J; Lopez-Garcia, Purificacion; Takaki, Yoshihiro; Nunoura, Takuro; Woyke, Tanja; Herndl, Gerhard J; Stepanauskas, Ramunas

2017-11-24

Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior, but the relevant taxa and energy sources remain enigmatic. We show evidence that nitrite-oxidizing bacteria affiliated with the Nitrospinae phylum are important in dark ocean chemoautotrophy. Single-cell genomics and community metagenomics revealed that Nitrospinae are the most abundant and globally distributed nitrite-oxidizing bacteria in the ocean. Metaproteomics and metatranscriptomics analyses suggest that nitrite oxidation is the main pathway of energy production in Nitrospinae. Microautoradiography, linked with catalyzed reporter deposition fluorescence in situ hybridization, indicated that Nitrospinae fix 15 to 45% of inorganic carbon in the mesopelagic western North Atlantic. Nitrite oxidation may have a greater impact on the carbon cycle than previously assumed. Copyright © 2017, American Association for the Advancement of Science.

Autecological Study of the Chemoautotroph Nitrobacter by Immunofluorescence

PubMed Central

Fliermans, C. B.; Bohlool, B. B.; Schmidt, E. L.

1974-01-01

Fluorescent antibodies (FA) prepared for Nitrobacter agilis and N. winogradskyi were highly reactive in homologous staining. Low-level cross-reactions between the two species were removed by adsorption. All 15 pure-culture isolates of Nitrobacter tested reacted strongly with either N. agilis FA or N. winogradskyi FA. All pure-culture isolates from soils were determined to be N. winogradskyi; those from Mammoth Cave sediments and a cattle waste oxidation ditch were N. agilis. No cross-reaction was found in extensive tests that included five isolates of Nitrosomonas europaea and 668 heterotrophic aerobic and anaerobic bacteria isolated from soil, sewage, and cave sites. The FA preparations were used to detect Nitrobacter species in Mammoth Cave sediments, in a cattle waste oxidation ditch, and in surface waters and sediments of a river and to observe that N. winogradskyi can outgrow N. agilis in enrichment culture. Images PMID:4589121

Nitrogen removal and electricity production at a double-chamber microbial fuel cell with cathode nitrite denitrification.

PubMed

Yu, Yangyang; Zhao, Jianqiang; Wang, Sha; Zhao, Huimin; Ding, Xiaoqian; Gao, Kun

2017-12-01

Double-chamber microbial fuel cell was applied to investigate the performance of the electricity production and nitrite denitrification through feeding nitrite into the cathode. Factors influencing denitrification performance and power production, such as external resistance, influent nitrite concentration and Nitrite Oxygen Bacteria inhibitors, were studied. The results show that when the concentration of nitrite nitrogen and external resistance were 100 mg L -1 and 10 Ω, respectively, the nitrite denitrification reached the best state. The NaN 3 can inhibit nitrite oxidation effectively; meanwhile, the nitrite denitrification with N 2 O as the final products was largely improved. The [Formula: see text] was reduced to [Formula: see text], causing the cathode denitrification coulombic efficiency to exceed 100%. In chemoautotrophic bio-nitrification, microorganisms may utilize H 2 O to oxidize nitrite under anaerobic conditions. Proteobacteria might play a major role in the process of denitrification in MFC.

Microbial Fossils from Terrestrial Subsurface Hydrothermal Environments: Examples and Implications for Mars

NASA Technical Reports Server (NTRS)

Hofmann, Beda A.; Farmer, Jack; Chang, Sherwood (Technical Monitor)

1997-01-01

The recognition of biological signatures in ancient epithermal deposits has special relevance for studies of early blaspheme evolution and in exploring for past life on Mars. Recently, proposals for the existence of an extensive subsurface blaspheme on Earth, dominated by chemoautotrophic microbial life, has gained prominence. However, reports of fossilized microbial remains, or biosedimentary structures (e.g. stromatolites) from the deposits of ancient subsurface systems, are rare. Microbial preservation is favoured where high population densities co-exist with rapid mineral precipitation. Near-surface epithetical systems with strong gradients in temperature and redox are good candidates for the abundant growth and fossilization of microorganisms, and are also favorable environments for the precipitation of ore minerals. Therefore, we might expect microbial remain, to be particularly well preserved in various kinds of hydrothermal and diagenetic mineral precipitates that formed below the upper temperature limit for life (approx. 120 C).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walsh, David A.; Zaikova, Elena; Howes, Charles L.

Oxygen minimum zones (OMZs), also known as oceanic"dead zones", are widespread oceanographic features currently expanding due to global warming and coastal eutrophication. Although inhospitable to metazoan life, OMZs support a thriving but cryptic microbiota whose combined metabolic activity is intimately connected to nutrient and trace gas cycling within the global ocean. Here we report time-resolved metagenomic analyses of a ubiquitous and abundant but uncultivated OMZ microbe (SUP05) closely related to chemoautotrophic gill symbionts of deep-sea clams and mussels. The SUP05 metagenome harbors a versatile repertoire of genes mediating autotrophic carbon assimilation, sulfur-oxidation and nitrate respiration responsive to a wide rangemore » of water column redox states. Thus, SUP05 plays integral roles in shaping nutrient and energy flow within oxygen-deficient oceanic waters via carbon sequestration, sulfide detoxification and biological nitrogen loss with important implications for marine productivity and atmospheric greenhouse control.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cannon, Gordon C.; Heinhorst, Sabine; Kerfeld, Cheryl A.

Cyanobacteria and some chemoautotrophic bacteria are able to grow in environments with limiting CO2 concentrations by employing a CO2-concentrating mechanism (CCM) that allows them to accumulate inorganic carbon in their cytoplasm to concentrations several orders of magnitude higher than that on the outside. The final step of this process takes place in polyhedral protein microcompartments known as carboxysomes, which contain the majority of the CO2-fixing enzyme, RubisCO. The efficiency of CO2 fixation by the sequestered RubisCO is enhanced by co-localization with a specialized carbonic anhydrase that catalyzes dehydration of the cytoplasmic bicarbonate and ensures saturation of RubisCO with its substrate,more » CO2. There are two genetically distinct carboxysome types that differ in their protein composition and in the carbonic anhydrase(s) they employ. Here we review the existing information concerning the genomics, structure and enzymology of these uniquely adapted carbonic anhydrases, which are of fundamental importance in the global carbon cycle.« less

Identification and characterization of multiple rubisco activases in chemoautotrophic bacteria

PubMed Central

Tsai, Yi-Chin Candace; Lapina, Maria Claribel; Bhushan, Shashi; Mueller-Cajar, Oliver

2015-01-01

Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) is responsible for almost all biological CO2 assimilation, but forms inhibited complexes with its substrate ribulose-1,5-bisphosphate (RuBP) and other sugar phosphates. The distantly related AAA+ proteins rubisco activase and CbbX remodel inhibited rubisco complexes to effect inhibitor release in plants and α-proteobacteria, respectively. Here we characterize a third class of rubisco activase in the chemolithoautotroph Acidithiobacillus ferrooxidans. Two sets of isoforms of CbbQ and CbbO form hetero-oligomers that function as specific activases for two structurally diverse rubisco forms. Mutational analysis supports a model wherein the AAA+ protein CbbQ functions as motor and CbbO is a substrate adaptor that binds rubisco via a von Willebrand factor A domain. Understanding the mechanisms employed by nature to overcome rubisco's shortcomings will increase our toolbox for engineering photosynthetic carbon dioxide fixation. PMID:26567524

The giant ciliate Zoothamnium niveum and its thiotrophic epibiont Candidatus Thiobios zoothamnicoli: a model system to study interspecies cooperation

PubMed Central

Bright, Monika; Espada-Hinojosa, Salvador; Lagkouvardos, Ilias; Volland, Jean-Marie

2014-01-01

Symbioses between chemoautotrophic sulfur-oxidizing (thiotrophic) bacteria and protists or animals are among the most diverse and prevalent in the ocean. They are extremely difficult to maintain in aquaria and no thiotrophic symbiosis involving an animal host has ever been successfully cultivated. In contrast, we have cultivated the giant ciliate Zoothamnium niveum and its obligate ectosymbiont Candidatus Thiobios zoothamnicoli in small flow-through aquaria. This review provides an overview of the host and the symbiont and their phylogenetic relationships. We summarize our knowledge on the ecology, geographic distribution and life cycle of the host, on the vertical transmission of the symbiont, and on the cultivation of this symbiosis. We then discuss the benefits and costs involved in this cooperation compared with other thiotrophic symbioses and outline our view on the evolution and persistence of this byproduct mutualism. PMID:24778630

Swept Away: Resuspension of Bacterial Mats Regulates Benthic-Pelagic Exchange of Sulfur

NASA Astrophysics Data System (ADS)

Grant, Jonathan; Bathmann, Ulrich V.

1987-06-01

Filaments and extracellular material from colorless sulfur bacteria (Beggiatoa spp.) form extensive white sulfur mats on surface sediments of coastal, oceanic, and even deep-sea environments. These chemoautotrophic bacteria oxidize soluble reduced sulfur compounds and deposit elemental sulfur, enriching the sulfur content of surface sediment fivefold over that of deeper sediments. Laboratory flume experiments with Beggiatoa mats from an intertidal sandflat (Nova Scotia) demonstrated that even slight erosion of sediment causes a flux of 160 millimoles of sulfur per square meter per hour, two orders of magnitude greater than the flux produced by sulfur transformations involving either sulfate reduction or sulfide oxidation by benthic bacteria. These experiments indicate that resuspension of sulfur bacterial mats by waves and currents is a rapid mechanism by which sediment sulfur is recycled to the water column. Benthic communities thus lose an important storage intermediate for reduced sulfur as well as a high-quality bacterial food source for benthic grazers.

Advances in metabolic engineering in the microbial production of fuels and chemicals from C1 gas.

PubMed

Humphreys, Christopher M; Minton, Nigel P

2018-04-01

The future sustainable production of chemicals and fuels from non-petrochemical sources, while at the same time reducing greenhouse gas (GHG) emissions, represent two of society's greatest challenges. Microbial chassis able to grow on waste carbon monoxide (CO) and carbon dioxide (CO 2 ) can provide solutions to both. Ranging from the anaerobic acetogens, through the aerobic chemoautotrophs to the photoautotrophic cyanobacteria, they are able to convert C1 gases into a range of chemicals and fuels which may be enhanced and extended through appropriate metabolic engineering. The necessary improvements will be facilitated by the increasingly sophisticated gene tools that are beginning to emerge as part of the Synthetic Biology revolution. These tools, in combination with more accurate metabolic and genome scale models, will enable C1 chassis to deliver their full potential. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Autotrophic microbial arsenotrophy in arsenic-rich soda lakes

USGS Publications Warehouse

Oremland, Ronald S.; Saltikov, Chad W.; Stolz, John F.; Hollibaugh, James T.

2017-01-01

A number of prokaryotes are capable of employing arsenic oxy-anions as either electron acceptors [arsenate; As(V)] or electron donors [arsenite; As(III)] to sustain arsenic-dependent growth (‘arsenotrophy’). A subset of these microorganisms function as either chemoautotrophs or photoautotrophs, whereby they gain sufficient energy from their redox metabolism of arsenic to completely satisfy their carbon needs for growth by autotrophy, that is the fixation of inorganic carbon (e.g. HCO3−) into their biomass. Here we review what has been learned of these processes by investigations we have undertaken in three soda lakes of the western USA and from the physiological characterizations of the relevant bacteria, which include the critical genes involved, such as respiratory arsenate reductase (arrA) and the discovery of its arsenite-oxidizing counterpart (arxA). When possible, we refer to instances of similar process occurring in other, less extreme ecosystems and by microbes other than haloalkaliphiles.

Predicting yields for autotrophic and cometabolic processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andrews, G.

1995-12-31

The goal of bioprocess engineering is to state how the optimum design and control strategy for a bioprocess follow from the metabolism of the particular microorganism. A necessary step toward this goal is to show how the parameters used in quantitative descriptions of a process (e.g., yield and maintenance coefficients) are related to those describing the metabolism [e.g., Y{sub ATP}, (P/O)]. The {open_quotes}yield equation{close_quotes} approach to this problem involves dividing metabolism into the separate pathways for catabolism, anabolism, respiration, and product formation and balancing the production and consumption of reducing equivalents and ATP. The general approach, demonstrated previously for heterotrophicmore » cell growth and products of fermentation, is illustrated by three new examples: the cell yield for chemoautotrophic iron-oxidizing bacteria, the cometabolic degradation of chloroform by methanotrophic bacteria, and the theoretical yield of succinic acid from glucose.« less

Carboxysomes: metabolic modules for CO 2 fixation

DOE PAGES

Turmo, Aiko; Gonzalez-Esquer, Cesar Raul; Kerfeld, Cheryl A.

2017-08-14

The carboxysome is a bacterial microcompartment encapsulating the enzymes carbonic anhydrase and ribulose-1,5-bisphosphate carboxylase/oxygenase. As the site of CO 2 fixation, it serves an essential role in the carbon dioxide concentrating mechanism of many chemoautotrophs and all cyanobacteria. Carboxysomes and other bacterial microcompartments self-assemble through specific protein–protein interactions that are typically mediated by conserved protein domains. In this review, we frame our current understanding of carboxysomes in the context of their component protein domains with their inherent function as the ‘building blocks’ of carboxysomes. These building blocks are organized in genetic modules (conserved chromosomal loci) that encode for carboxysomes andmore » ancillary proteins essential for the integration of the organelle with the rest of cellular metabolism. This conceptual framework provides the foundation for ‘plug-and-play’ engineering of carboxysomes as CO 2 fixation modules in a variety of biotechnological applications.« less

Rediscovered and new perisphaerine cockroaches from SW China with a review of subfamilial diagnosis (Blattodea: Blaberidae).

PubMed

Li, Xin-Ran; Wang, Li-Li; Wang, Zong-Qing

2018-04-17

The taxonomic records of Chinese perisphaerine cockroaches were scattered in literature, and therefore a dedicated study is desired to update our knowledge. This paper reviews the subfamilial diagnosis and Chinese species, mostly from southwestern China. We provide high-definition habitus photos and drawings, the latter emphasizes the genitalia of both sexes, which are generalized with diagrams, abstracted from specimens examined. A total of 18 species are recorded in four genera, including Perisphaerus, or pill cockroach, the type genus of the subfamily. Two new genera and three new species are proposed: Achatiblatta achates gen. sp. nov., Frumentiforma frumentiformis gen. sp. nov., and Pseudoglomeris montana sp. nov.. Pseudoglomeris has five new junior synonyms: Corydidarum, Trichoblatta, Kurokia, Glomerexis, and Glomeriblatta; the following combinations are thus revived or new: Ps. aerea comb. nov., Ps. angustifolia comb. nov., Ps. beybienkoi comb. nov., Ps. fallax comb. nov., Ps. magnifica comb. rev., Ps. montshadskii comb. nov., Ps. nigra comb. nov., Ps. sculpta comb. nov., Ps. semisulcata comb. rev., Ps. tibetana comb. nov., and Ps. valida moderata comb. nov.. The following species are revalidated and combinations revived: Pe. pygmaeus comb. rev., Ps. dubia comb. sp. rev., and Ps. planiuscla comb. sp. rev.

Reef fishes can recognize bleached habitat during settlement: sea anemone bleaching alters anemonefish host selection

PubMed Central

Scott, Anna; Dixson, Danielle L.

2016-01-01

Understanding how bleaching impacts the settlement of symbiotic habitat specialists and whether there is flexibility in settlement choices with regard to habitat quality is essential given our changing climate. We used five anemonefishes (Amphiprion clarkii, Amphiprion latezonatus, Amphiprion ocellaris, Amphiprion percula and Premnas biaculeatus) and three host sea anemones (Entacmaea quadricolor, Heteractis crispa and Heteractis magnifica) in paired-choice flume experiments to determine whether habitat naive juveniles have the olfactory capabilities to distinguish between unbleached and bleached hosts, and how this may affect settlement decisions. All anemonefishes were able to distinguish between bleached and unbleached hosts, and responded only to chemical cues from species-specific host anemones irrespective of health status, indicating a lack of flexibility in host use. While bleached hosts were selected as habitat, this occurred only when unbleached options were unavailable, with the exception of A. latezonatus, which showed strong preferences for H. crispa regardless of health. This study highlights the potential deleterious indirect impacts of declining habitat quality during larval settlement in habitat specialists, which could be important in the field, given that bleaching events are becoming increasingly common. PMID:27226472

Reef fishes can recognize bleached habitat during settlement: sea anemone bleaching alters anemonefish host selection.

PubMed

Scott, Anna; Dixson, Danielle L

2016-05-25

Understanding how bleaching impacts the settlement of symbiotic habitat specialists and whether there is flexibility in settlement choices with regard to habitat quality is essential given our changing climate. We used five anemonefishes (Amphiprion clarkii, Amphiprion latezonatus, Amphiprion ocellaris, Amphiprion percula and Premnas biaculeatus) and three host sea anemones (Entacmaea quadricolor, Heteractis crispa and Heteractis magnifica) in paired-choice flume experiments to determine whether habitat naive juveniles have the olfactory capabilities to distinguish between unbleached and bleached hosts, and how this may affect settlement decisions. All anemonefishes were able to distinguish between bleached and unbleached hosts, and responded only to chemical cues from species-specific host anemones irrespective of health status, indicating a lack of flexibility in host use. While bleached hosts were selected as habitat, this occurred only when unbleached options were unavailable, with the exception of A. latezonatus, which showed strong preferences for H. crispa regardless of health. This study highlights the potential deleterious indirect impacts of declining habitat quality during larval settlement in habitat specialists, which could be important in the field, given that bleaching events are becoming increasingly common. © 2016 The Author(s).

Hatchery production of the clownfish Amphiprion nigripes at Agatti Island, Lakshadweep, India.

PubMed

Kumar, T T Ajith; Gopi, M; Dhaneesh, K V; Vinoth, R; Ghosh, S; Balasubramanian, T; Shunmugaraj, T

2012-05-01

Healthy individuals of matured clownfish, Amphiprion nigripes and sea anemone, Heteractis magnifica were collected from the Agatti island lagoon by snorkeling. During 'conditioning' for 3 months, pair formation occurred and the same were transferred to rectangular fiber glass spawning tanks of 10001 capacity. Suitable water quality parameters were maintained. The fishes were fed with tuna eggs, boiled clam meat, squid, octopus and trash fish thrice in a day. Reproductive behaviour and embryonic development were documented. Spawning took place in between 0900 - 1100 hr and hatched-out occurs, after sunset following an incubation period of 8-9 days. Size of the newly laid egg was 2.0-2.2 mm in length and 1.0-1.2 mm in width. The larval rearing tanks were maintained with UV-treated water and followed the optimal physico-chemical parameters as in the parent tanks. The different light regimes and diets were used for the successful larval rearing. The maximum larval survival (61%) was achieved at the photoperiod of 24 L/0D. Within 15-17 days, the larvae metamorphosed and took up parent colouration and comparatively high growth rate was observed when fed on algae enriched rotifer than those with poly unsaturated fatty acid (PUFA).

Mineralogy of Surface Serpentinite Outcrops in the Coast Range Ophiolite: Implications for the Deep Biosphere and Astrobiology

NASA Astrophysics Data System (ADS)

Mccann, A. R.; Cardace, D.; Carnevale, D.; Ehlmann, B. L.

2011-12-01

California contains a number of ultramafic (Fe- and Mg rich) rock bodies, including the Coast Range Ophiolite, a block of oceanic crust and upper mantle tectonically emplaced onto land. These ultramafic rocks are primarily composed of olivine and pyroxene, both of which are stable at the high temperatures and pressures in the deep subsurface where they crystallize but become unstable at low temperature and low pressure conditions near the surface. They are highly reduced rocks, creating chemical disequilibria, which can theoretically provide energy to chemoautotrophic organisms. Serpentinization (serpentine-forming) reactions between the rocks and water produce hydrogen molecules, which can be metabolized by diverse organisms. Earth and Mars have shown evidence of similar early geologic histories, possibly with widespread reducing habitable environments (Schulte et al., 2006). Recent data from the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) have shown serpentine-bearing outcrops near Nili Fossae (21 N, 282 W) and elsewhere in Mars' cratered highlands. Serpentine-bearing outcrops are rare, but their presence confirms that such systems involving the aqueous alteration of ultramafic rocks were active in the past (specifically during the Noachian epoch (older than ~3.7 billion years), possibly producing aqueous habitats suitable for chemoautotrophic life (Ehlmann et al., 2010). Remotely sensed data cannot confirm whether there is active serpentinization on Mars, however exposed, presently serpentinizing ultramafics in terrestrial ophiolites such as those of the California Coast Range provide points of comparison for similar Martian rocks. Volume expansion during serpentinization fractures the host rock, exposing new reaction surfaces, allowing further serpentinization. If subsurface liquid water is present on Mars, serpentinization may still be occurring. We will provide x-ray diffraction and petrographic data for surface serpentinites from the Coast Range Ophiolite, along with aerial-view maps, which will be compared with imagery and data for recently confirmed serpentinite exposures in the Nili Fossae region of the Martian surface. A summary table of terrestrial microbes (and their metabolisms) detected in serpentinite groundwaters will be provided, to add specificity to candidate subterranean life forms on Mars, be they active presently or in the planet's history. Ehlmann et al. 2010. GRL 37:1-5 Schulte et al. 2006. Astrobiology 6(2):364-376

Parasitic diseases of camels in Iran (1931–2017) – a literature review

PubMed Central

Sazmand, Alireza; Joachim, Anja

2017-01-01

Parasitic diseases of camels are major causes of impaired milk and meat production, decreases in performance or even death. Some camel parasites also represent a threat to human health. About 171,500 one-humped camels (Camelus dromedarius) and 100–300 two-humped camels (Camelus bactrianus) live in Iran. Knowledge of the biodiversity of their parasites is still limited. The present review covers all information about camel parasitic diseases in Iran published as dissertations and in both Iranian and international journals from 1931 to February 2017. Ten genera of Protozoa (Trypanosoma, Eimeria, Cryptosporidium, Toxoplasma, Neospora, Sarcocystis, Besnoitia, Theileria, Babesia and Balantidium), 48 helminth species detected in the digestive system, including three species of Trematoda, four species of Cestoda, and 41 species of Nematoda, as well as helminths from other organs – Echinococcus spp., Dictyocaulus filaria, Thelazia leesei, Dipetalonema evansi and Onchocerca fasciata – have so far been described in Iranian camels. Furthermore, 13 species of hard ticks, mange mites, the myiasis flies Cephalopina titillator and Wohlfahrtia magnifica, and immature stages of the Pentastomida Linguatula serrata have also been reported from camels of Iran. Camel parasitic diseases are a major issue in Iran in terms of economics and public health. The present review offers information for an integrated control programme against economically relevant parasites of camels. PMID:28617666

Mars Analog Rio Tinto Experiment (MARTE): 2003 Drilling Campaign to Search for a Subsurface Biosphere at Rio Tinto Spain

NASA Technical Reports Server (NTRS)

Stoker, Carol; Dunagan, Stephen; Stevens, Todd; Amils, Ricardo; Gomez-Elvira, Javier; Fernandez, David; Hall, James; Lynch, Kennda; Cannon, Howard; Zavaleta, Jhony

2004-01-01

The MARTE (Mars Astrobiology Research and Technology Experiment) project, an ASTEP field experiment, is exploring for a hypothesized subsurface anaerobic chemoautotrophic biosphere in the region of the Tinto River- or Rio Tinto- in southwestern Spain. It is also demonstrating technology needed to search for a subsurface biosphere on Mars. The project has three primary objectives: (1) search for and characterize subsurface life at Rio Tinto along with the physical and chemical properties and sustaining energy sources of its environment, (2) perform a high fidelity simulation of a robotic Mars drilling mission to search for life, and (3) demonstrate the drilling, sample handling, and instrument technologies relevant to searching for life on Mars. The simulation of the robotic drilling mission is guided by the results of the aseptic drilling campaign to search for life at Rio Tinto. This paper describes results of the first phase of the aseptic drilling campaign.

Sequestration and utilization of carbon dioxide by chemical and biological methods for biofuels and biomaterials by chemoautotrophs: Opportunities and challenges.

PubMed

Thakur, Indu Shekhar; Kumar, Manish; Varjani, Sunita J; Wu, Yonghong; Gnansounou, Edgard; Ravindran, Sindhu

2018-05-01

To meet the CO 2 emission reduction targets, carbon dioxide capture and utilization (CCU) comes as an evolve technology. CCU concept is turning into a feedstock and technologies have been developed for transformation of CO 2 into useful organic products. At industrial scale, utilization of CO 2 as raw material is not much significant as compare to its abundance. Mechanisms in nature have evolved for carbon concentration, fixation and utilization. Assimilation and subsequent conversion of CO 2 into complex molecules are performed by the photosynthetic and chemolithotrophic organisms. In the last three decades, substantial research is carry out to discover chemical and biological conversion of CO 2 in various synthetic and biological materials, such as carboxylic acids, esters, lactones, polymer biodiesel, bio-plastics, bio-alcohols, exopolysaccharides. This review presents an over view of catalytic transformation of CO 2 into biofuels and biomaterials by chemical and biological methods. Copyright © 2018 Elsevier Ltd. All rights reserved.

[Resting forms of gram negative chemolithoautotrophic bacteria Thioalkalivibrio versutus and Thioalkalimicrobium aerophilum].

PubMed

Loĭko, N G; Soina, V S; Sorokin, D Iu; Mitiushina, L L; El'-Registan, G I

2003-01-01

The haloalkaliphilic chemoautotrophic gram-negative bacteria Thioalkalivibrio versutus, strain AL2, and Thioalkalimicrobium aerophilum, strain AL3, were shown to possess the capacity to produce resting forms, namely cyst-like refractile cells (CRC), whose production was controlled by the level of the d1 extracellular factors, exhibiting the function of anabiosis autoinducers. The conditions were elucidated that promoted the formation of CRC in the developmental cycles of the cultures studied, in condensed cell suspensions undergoing autolysis, and under the action of exogenously introduced chemical analogues of anabiosis autoinducers (alkylhydroxybenzenes). The peculiarities of the fine structure of the resting cells obtained were studied. Distinctions were revealed (with respect to viability and thermotolerance) between the CRC formed under different conditions. The relationship between the growth strategy and survival strategy of extremophilic bacteria is discussed with taking into account the effect of the d1 autoregulatory factors. A new model of CRC formation is proposed: CRC production in the life cycle of bacteria developing under conditions of increased concentration of anabiosis autoinducers.

High-temperature water–rock interactions and hydrothermal environments in the chondrite-like core of Enceladus

PubMed Central

Sekine, Yasuhito; Shibuya, Takazo; Postberg, Frank; Hsu, Hsiang-Wen; Suzuki, Katsuhiko; Masaki, Yuka; Kuwatani, Tatsu; Mori, Megumi; Hong, Peng K.; Yoshizaki, Motoko; Tachibana, Shogo; Sirono, Sin-iti

2015-01-01

It has been suggested that Saturn's moon Enceladus possesses a subsurface ocean. The recent discovery of silica nanoparticles derived from Enceladus shows the presence of ongoing hydrothermal reactions in the interior. Here, we report results from detailed laboratory experiments to constrain the reaction conditions. To sustain the formation of silica nanoparticles, the composition of Enceladus' core needs to be similar to that of carbonaceous chondrites. We show that the presence of hydrothermal reactions would be consistent with NH3- and CO2-rich plume compositions. We suggest that high reaction temperatures (>50 °C) are required to form silica nanoparticles whether Enceladus' ocean is chemically open or closed to the icy crust. Such high temperatures imply either that Enceladus formed shortly after the formation of the solar system or that the current activity was triggered by a recent heating event. Under the required conditions, hydrogen production would proceed efficiently, which could provide chemical energy for chemoautotrophic life. PMID:26506464

Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Lamellomorpha sp. indicated by metagenomics

NASA Astrophysics Data System (ADS)

Li, Zhi-Yong; Wang, Yue-Zhu; He, Li-Ming; Zheng, Hua-Jun

2014-01-01

The whole metabolism of a sponge holobiont and the respective contributions of prokaryotic and eukaryotic symbionts and their associations with the sponge host remain largely unclear. Meanwhile, compared with shallow water sponges, deep-sea sponges are rarely understood. Here we report the metagenomic exploration of deep-sea sponge Lamellomorpha sp. at the whole community level. Metagenomic data showed phylogenetically diverse prokaryotes and eukaryotes in Lamellomorpha sp.. MEGAN and gene enrichment analyses indicated different metabolic potentials of prokaryotic symbionts from eukaryotic symbionts, especially in nitrogen and carbon metabolisms, and their molecular interactions with the sponge host. These results supported the hypothesis that prokaryotic and eukaryotic symbionts have different ecological roles and relationships with sponge host. Moreover, vigorous denitrification, and CO2 fixation by chemoautotrophic prokaryotes were suggested for this deep-sea sponge. The study provided novel insights into the respective potentials of prokaryotic and eukaryotic symbionts and their associations with deep-sea sponge Lamellomorpha sp..

Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi indicated by metagenomics

PubMed Central

Li, Zhi-Yong; Wang, Yue-Zhu; He, Li-Ming; Zheng, Hua-Jun

2014-01-01

The whole metabolism of a sponge holobiont and the respective contributions of prokaryotic and eukaryotic symbionts and their associations with the sponge host remain largely unclear. Meanwhile, compared with shallow water sponges, deep-sea sponges are rarely understood. Here we report the metagenomic exploration of deep-sea sponge Neamphius huxleyi at the whole community level. Metagenomic data showed phylogenetically diverse prokaryotes and eukaryotes in Neamphius huxleyi. MEGAN and gene enrichment analyses indicated different metabolic potentials of prokaryotic symbionts from eukaryotic symbionts, especially in nitrogen and carbon metabolisms, and their molecular interactions with the sponge host. These results supported the hypothesis that prokaryotic and eukaryotic symbionts have different ecological roles and relationships with sponge host. Moreover, vigorous denitrification, and CO2 fixation by chemoautotrophic prokaryotes were suggested for this deep-sea sponge. The study provided novel insights into the respective potentials of prokaryotic and eukaryotic symbionts and their associations with deep-sea sponge Neamphius huxleyi. PMID:24463735

Ecophysiology of "halarsenatibacter silvermanii" strain SLAS-1T, gen. nov., sp. nov., a facultative chemoautotrophic arsenate respirer from salt-saturated Searles Lake, California

USGS Publications Warehouse

Blum, J.S.; Han, S.; Lanoil, B.; Saltikov, C.; Witte, B.; Tabita, F.R.; Langley, S.; Beveridge, T.J.; Jahnke, L.; Oremland, R.S.

2009-01-01

Searles Lake occupies a closed basin harboring salt-saturated, alkaline brines that have exceptionally high concentrations of arsenic oxyanions. Strain SLAS-1T was previously isolated from Searles Lake (R. S. Oremland, T. R. Kulp, J. Switzer Blum, S. E. Hoeft, S. Baesman, L. G. Miller, and J. F. Stolz, Science 308:1305-1308, 2005). We now describe this extremophile with regard to its substrate affinities, its unusual mode of motility, sequenced arrABD gene cluster, cell envelope lipids, and its phylogenetic alignment within the order Halanaero-bacteriales, assigning it the name "Halarsenatibacter silvermanii" strain SLAS-1T. We also report on the substrate dynamics of an anaerobic enrichment culture obtained from Searles Lake that grows under conditions of salt saturation and whose members include a novel sulfate reducer of the order Desulfovibriales, the archaeon Halorhabdus utahensis, as well as a close homolog of strain SLAS-1T. Copyright ?? 2009, American Society for Microbiology. All Rights Reserved.

The history of aerobic ammonia oxidizers: from the first discoveries to today.

PubMed

Monteiro, Maria; Séneca, Joana; Magalhães, Catarina

2014-07-01

Nitrification, the oxidation of ammonia to nitrite and nitrate, has long been considered a central biological process in the global nitrogen cycle, with its first description dated 133 years ago. Until 2005, bacteria were considered the only organisms capable of nitrification. However, the recent discovery of a chemoautotrophic ammonia-oxidizing archaeon, Nitrosopumilus maritimus, changed our concept of the range of organisms involved in nitrification, highlighting the importance of ammonia-oxidizing archaea (AOA) as potential players in global biogeochemical nitrogen transformations. The uniqueness of these archaea justified the creation of a novel archaeal phylum, Thaumarchaeota. These recent discoveries increased the global scientific interest within the microbial ecology society and have triggered an analysis of the importance of bacterial vs archaeal ammonia oxidation in a wide range of natural ecosystems. In this mini review we provide a chronological perspective of the current knowledge on the ammonia oxidation pathway of nitrification, based on the main physiological, ecological and genomic discoveries.

Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi [corrected]. indicated by metagenomics.

PubMed

Li, Zhi-Yong; Wang, Yue-Zhu; He, Li-Ming; Zheng, Hua-Jun

2014-01-27

The whole metabolism of a sponge holobiont and the respective contributions of prokaryotic and eukaryotic symbionts and their associations with the sponge host remain largely unclear. Meanwhile, compared with shallow water sponges, deep-sea sponges are rarely understood. Here we report the metagenomic exploration of deep-sea sponge Neamphius huxleyi [corrected] . at the whole community level. Metagenomic data showed phylogenetically diverse prokaryotes and eukaryotes in Neamphius huxleyi [corrected]. MEGAN and gene enrichment analyses indicated different metabolic potentials of prokaryotic symbionts from eukaryotic symbionts, especially in nitrogen and carbon metabolisms, and their molecular interactions with the sponge host. These results supported the hypothesis that prokaryotic and eukaryotic symbionts have different ecological roles and relationships with sponge host. Moreover, vigorous denitrification, and CO2 fixation by chemoautotrophic prokaryotes were suggested for this deep-sea sponge. The study provided novel insights into the respective potentials of prokaryotic and eukaryotic symbionts and their associations with deep-sea sponge Neamphius huxleyi [corrected].

Ecophysiology of "Halarsenatibacter silvermanii" strain SLAS-1T, gen. nov., sp. nov., a facultative chemoautotrophic arsenate respirer from salt-saturated Searles Lake, California.

PubMed

Blum, Jodi Switzer; Han, Sukkyun; Lanoil, Brian; Saltikov, Chad; Witte, Brian; Tabita, F Robert; Langley, Sean; Beveridge, Terry J; Jahnke, Linda; Oremland, Ronald S

2009-04-01

Searles Lake occupies a closed basin harboring salt-saturated, alkaline brines that have exceptionally high concentrations of arsenic oxyanions. Strain SLAS-1(T) was previously isolated from Searles Lake (R. S. Oremland, T. R. Kulp, J. Switzer Blum, S. E. Hoeft, S. Baesman, L. G. Miller, and J. F. Stolz, Science 308:1305-1308, 2005). We now describe this extremophile with regard to its substrate affinities, its unusual mode of motility, sequenced arrABD gene cluster, cell envelope lipids, and its phylogenetic alignment within the order Halanaerobacteriales, assigning it the name "Halarsenatibacter silvermanii" strain SLAS-1(T). We also report on the substrate dynamics of an anaerobic enrichment culture obtained from Searles Lake that grows under conditions of salt saturation and whose members include a novel sulfate reducer of the order Desulfovibriales, the archaeon Halorhabdus utahensis, as well as a close homolog of strain SLAS-1(T).

Investigation on energy conversion technology using biochemical reaction elements, 2

NASA Astrophysics Data System (ADS)

1994-03-01

For measures taken for resource/energy and environmental issues, a study is made on utilization of microbial biochemical reaction. As a reaction system using chemical energy, cited is production of petroleum substitution substances and food/feed by CO2 fixation using hydrogen energy and hydrogen bacteria. As to photo energy utilization, regarded as promising are CO2 fixation using photo energy and microalgae, and production of hydrogen and useful carbon compound using photosynthetic organisms. As living organism/electric energy interconversion, cited is the culture of chemoautotrophic bacteria which fix CO2 using electric energy. For enhancing its conversion efficiency, it is important to develop a technology of gene manipulation of the bacteria and a system to use functional biochemical elements adaptable to the electrode reaction. With regard to utilization of the microorganism metabolic function, the paper presents emission of soluble nitrogen in the hydrosphere into the atmosphere using denitrifying bacteria, removal of phosphorus, reduction in environmental pollution caused by heavy metal dilute solutions, and recovery as resources, etc.

High-temperature water-rock interactions and hydrothermal environments in the chondrite-like core of Enceladus.

PubMed

Sekine, Yasuhito; Shibuya, Takazo; Postberg, Frank; Hsu, Hsiang-Wen; Suzuki, Katsuhiko; Masaki, Yuka; Kuwatani, Tatsu; Mori, Megumi; Hong, Peng K; Yoshizaki, Motoko; Tachibana, Shogo; Sirono, Sin-iti

2015-10-27

It has been suggested that Saturn's moon Enceladus possesses a subsurface ocean. The recent discovery of silica nanoparticles derived from Enceladus shows the presence of ongoing hydrothermal reactions in the interior. Here, we report results from detailed laboratory experiments to constrain the reaction conditions. To sustain the formation of silica nanoparticles, the composition of Enceladus' core needs to be similar to that of carbonaceous chondrites. We show that the presence of hydrothermal reactions would be consistent with NH3- and CO2-rich plume compositions. We suggest that high reaction temperatures (>50 °C) are required to form silica nanoparticles whether Enceladus' ocean is chemically open or closed to the icy crust. Such high temperatures imply either that Enceladus formed shortly after the formation of the solar system or that the current activity was triggered by a recent heating event. Under the required conditions, hydrogen production would proceed efficiently, which could provide chemical energy for chemoautotrophic life.

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine

PubMed Central

E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-01-01

ABSTRACT The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. IMPORTANCE This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. PMID:27663031

Biosygnatures on olivines in search of past life on Mars

NASA Astrophysics Data System (ADS)

Jakus, Natalia; Manecki, Maciej; Faehnrich, Karol; Młynarska, Maria; Słupski, Paweł

2017-04-01

Biosignatures indicate past and present activity of living organisms. Only inorganic biosignatures, e.g. results of interactions between the minerals and the microorganisms in Martian soils could resist harsh environmental conditions on Mars. However, it may be difficult to distinguish the traces of the organism activities from the effects of "natural" chemical and physical processes. In this study, an acidiophilic, chemoautotrophic, iron-oxidizing bacteria Acidithiobacillus ferrooxidans were incubated with magnesium-iron silicate (olivine) crystals to identify the potential development of biogenic textures on the surface. The Mg-rich olivines were separated from the gabbro rock (Trodos, Cyprus). The isometric crystals were up to 2 mm in size. All the grains were cleaned in ultrasonic bath and fixed on the epoxy stubs. This enabled the observation of the very same surfaces before and after the experiments allowing inspection of natural etch pits and weathering patterns present before inoculation as well as the forms resulting from the experiments. The stubs with the olivines were sterilized with ethanol prior to the experiments. Bacteria were isolated from old pyrite mine in Klucze near Olkusz (Southern Poland). A liquid media K9 was used through the experiments (Silverman and Ludgren, 1959). The experiments were run in triplicates. Olivine grains were placed in the inoculated medium and incubated for 7 days at 28 C. An abiotic experiment was run as control. Additionally, the experiments in modified (iron deficient) medium were designed to stimulate potential active scavenging for Fe by bacteria-mediated dissolution. In the Fe-deficient medium, the negligible amount of iron was present only to initiate the bacteria growth: the only source of Fe was the olivine grain throughout the experiment. After 7 days of incubation the olivine grains were removed and air-dried. The alterations of the crystals by both, purely inorganic and biologically mediated dissolution were investigated with the use of scanning electron microscopy (SEM) with EDS microanalyzer. Any alteration of mineral surface resulting from mineral-microbes interaction was considered as a biosignature. In the standard Fe-rich K9 medium, occasional precipitation of the sulfate phase was observed. There is no evidence for the microbial control on this process. Formation of etch pits was observed in both, Fe-rich and Fe-deficient experiments, in the presence and in the absence of bacteria. The dissolution patterns were indistinguishable. Therefore, the experiments resulting in formation of the biofilm will be designed in future. SILVERMAN M.P., LUNDGREN D.G., 1959. Studies on the chemoautotrophic iron bacterium Ferrobacillus ferrooxidans. An improved medium and a harvesting procedure for securing high cell yields.

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine.

PubMed

Zeng, Xian-Chun; E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-12-15

The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

DNA barcoding for species identification in deep-sea clams (Mollusca: Bivalvia: Vesicomyidae).

PubMed

Liu, Jun; Zhang, Haibin

2018-01-15

Deep-sea clams (Bivalvia: Vesicomyidae) have been found in reduced environments over the world oceans, but taxonomy of this group remains confusing at species and supraspecific levels due to their high-morphological similarity and plasticity. In the present study, we collected mitochondrial COI sequences to evaluate the utility of DNA barcoding on identifying vesicomyid species. COI dataset identified 56 well-supported putative species/operational taxonomic units (OTUs), approximately covering half of the extant vesicomyid species. One species (OTU2) was first detected, and may represent a new species. Average distances between species ranged from 1.65 to 29.64%, generally higher than average intraspecific distances (0-1.41%) when excluding Pliocardia sp.10 cf. venusta (average intraspecific distance 1.91%). Local barcoding gap existed in 33 of the 35 species when comparing distances of maximum interspecific and minimum interspecific distances with two exceptions (Abyssogena southwardae and Calyptogena rectimargo-starobogatovi). The barcode index number (BIN) system determined 41 of the 56 species/OTUs, each with a unique BIN, indicating their validity. Three species were found to have two BINs, together with their high level of intraspecific variation, implying cryptic diversity within them. Although fewer 16 S sequences were collected, similar results were obtained. Nineteen putative species were determined and no overlap observed between intra- and inter-specific variation. Implications of DNA barcoding for the Vesicomyidae taxonomy were then discussed. Findings of this study will provide important evidence for taxonomic revision in this problematic clam group, and accelerate the discovery of new vesicomyid species in the future.

Parasitic diseases of camels in Iran (1931-2017) - a literature review.

PubMed

Sazmand, Alireza; Joachim, Anja

2017-01-01

Parasitic diseases of camels are major causes of impaired milk and meat production, decreases in performance or even death. Some camel parasites also represent a threat to human health. About 171,500 one-humped camels (Camelus dromedarius) and 100-300 two-humped camels (Camelus bactrianus) live in Iran. Knowledge of the biodiversity of their parasites is still limited. The present review covers all information about camel parasitic diseases in Iran published as dissertations and in both Iranian and international journals from 1931 to February 2017. Ten genera of Protozoa (Trypanosoma, Eimeria, Cryptosporidium, Toxoplasma, Neospora, Sarcocystis, Besnoitia, Theileria, Babesia and Balantidium), 48 helminth species detected in the digestive system, including three species of Trematoda, four species of Cestoda, and 41 species of Nematoda, as well as helminths from other organs - Echinococcus spp., Dictyocaulus filaria, Thelazia leesei, Dipetalonema evansi and Onchocerca fasciata - have so far been described in Iranian camels. Furthermore, 13 species of hard ticks, mange mites, the myiasis flies Cephalopina titillator and Wohlfahrtia magnifica, and immature stages of the Pentastomida Linguatula serrata have also been reported from camels of Iran. Camel parasitic diseases are a major issue in Iran in terms of economics and public health. The present review offers information for an integrated control programme against economically relevant parasites of camels. © A. Sazmand & A. Joachim, published by EDP Sciences, 2017.

Purification and characterization of gigantoxin-4, a new actinoporin from the sea anemone Stichodactyla gigantea.

PubMed

Hu, Bo; Guo, Wei; Wang, Liang-Hua; Wang, Jian-Guang; Liu, Xiao-Yu; Jiao, Bing-Hua

2011-01-01

A new Cytolysin, termed as Gigantoxin-4, was isolated from the sea anemone Stichodactyla gigantea and found to be highly homologous with Cytolysin-3 (HMg III) from Heteractis magnifica, RTX-A from Radianthus macrodactylus, and Sticholysin-1 (St I) and Sticholysin-2 (St II) from Stichodactyla helianthus (homology 82%, 86%, 82% and 86% respectively). Its 20 N-terminal residues were identified and the full-length cDNA sequence was obtained by reverse transcription-polymerase chain reaction (RT-PCR). Multiple sequence alignments with other Cytolysins of the actinoporin family clearly indicated that Gigantoxin-4 belongs to this protein family. SDS-PAGE electrophoresis showed that this new actinoporin had a molecular mass of about 19 kDa, and possessed a high hemolytic activity to human erythrocytes (HA(50)= 40 ng/ml), which was inhibited by pre-incubation with sphingomyelin (SM) or SM-cholesterol mixtures. Our in vivo experiments showed that Gigantoxin-4 had wide toxicity to the rat cardiovascular system and the respiratory system. A concentration of 30 μg/kg Gigantoxin-4, i.v. produced a positive inotropic effect on the rat heart although final cardiovascular failure was inevitable, and 60 μg/kg Gigantoxin-4 caused respiratory arrest rapidly resulting in rat death. HE staining indicated pathological changes in various organs and tissues after i.v. administration of Gigantoxin-4.

Anemone bleaching increases the metabolic demands of symbiont anemonefish.

PubMed

Norin, Tommy; Mills, Suzanne C; Crespel, Amélie; Cortese, Daphne; Killen, Shaun S; Beldade, Ricardo

2018-04-11

Increased ocean temperatures are causing mass bleaching of anemones and corals in the tropics worldwide. While such heat-induced loss of algal symbionts (zooxanthellae) directly affects anemones and corals physiologically, this damage may also cascade on to other animal symbionts. Metabolic rate is an integrative physiological trait shown to relate to various aspects of organismal performance, behaviour and locomotor capacity, and also shows plasticity during exposure to acute and chronic stressors. As climate warming is expected to affect the physiology, behaviour and life history of animals, including ectotherms such as fish, we measured if residing in bleached versus unbleached sea anemones ( Heteractis magnifica ) affected the standard (i.e. baseline) metabolic rate and behaviour (activity) of juvenile orange-fin anemonefish ( Amphiprion chrysopterus ) . Metabolic rate was estimated from rates of oxygen uptake [Formula: see text], and the standard metabolic rate [Formula: see text] of anemonefish from bleached anemones was significantly higher by 8.2% compared with that of fish residing in unbleached anemones, possibly due to increased stress levels. Activity levels did not differ between fish from bleached and unbleached anemones. As [Formula: see text] reflects the minimum cost of living, the increased metabolic demands may contribute to the negative impacts of bleaching on important anemonefish life history and fitness traits observed previously (e.g. reduced spawning frequency and lower fecundity). © 2018 The Author(s).

Beyond the vent: New perspectives on hydrothermal plumes and pelagic biology

NASA Astrophysics Data System (ADS)

Phillips, Brennan T.

2017-03-01

Submarine hydrothermal vent fields introduce buoyant plumes of chemically altered seawater to the deep-sea water column. Chemoautotrophic microbes exploit this energy source, facilitating seafloor-based primary production that evidence suggests may transfer to pelagic consumers. While most hydrothermal plumes have relatively small volumes, there are recent examples of large-scale plume events associated with periods of eruptive activity, which have had a pronounced effect on water-column biology. This correlation suggests that hydrothermal plumes may have influenced basin-scale ocean chemistry during periods of increased submarine volcanism during the Phanerozoic eon. This paper synthesizes a growing body of scientific evidence supporting the hypothesis that hydrothermal plumes are the energetic basis of unique deep-sea pelagic food webs. While many important questions remain concerning the biology of hydrothermal plumes, this discussion is not present in ongoing management efforts related to seafloor massive sulfide (SMS) mining. Increased research efforts, focused on high-resolution surveys of midwater biology relative to plume structures, are recommended to establish baseline conditions and monitor the impact of future mining-based disturbances to the pelagic biosphere.

Food Web Structure at South Su, Solwara 1 and Solwara 8 Hydrothermal Vent Sites (Manus Basin)

NASA Astrophysics Data System (ADS)

Honig, D. L.; Hsing, P.; Jones, R.; Schultz, T.; Sobel, A.; Thaler, A.; van Dover, C. L.

2008-12-01

A robust understanding of food webs in chemoautotrophically based hydrothermal vent ecosystems requires quantifying the input of local bacterial chemoautoptrophic production vs. photosynthetically derived debris from surface waters. As an initial step towards this goal for vent communities in Papua New Guinea's Manus Basin, we use isotopic ratios of carbon, nitrogen and sulfur to describe trophic relations among 17 invertebrate genera collected in July 2008 at the Solwara 1, Solwara 8 and South Su hydrothermal vent beds. Prior stable isotope work by Erickson, Macko and Van Dover (unpublished) at Manus Basin vent sites suggests that we will see relatively depleted ä13C and ä15N values for the primary consumers Ifremeria, Alviniconcha and Olgasolaris compared to secondary consumers like the mobile, scavenging genera Munidopsis, Austinograea, Alvinocaris and Chorocaris, sessile suspension feeders of the genera Eochinolasmus and Vulcanolepas, and the predatory sponge Abyssocladia. We further hypothesize that mobile fauna will exhibit greater within-genus variance of ä13C, ä15N and ä34S values than sessile genera due to mobile organisms' ability to forage for photosynthetically derived detritus.

The Structure of Isolated Synechococcus Strain WH8102 Carboxysomes as Revealed by Electron Cryotomography

PubMed Central

Iancu, Cristina V.; Ding, H. Jane; Morris, Dylan M.; Dias, D. Prabha; Gonzales, Arlene D.; Martino, Anthony; Jensen, Grant J.

2007-01-01

Carboxysomes are organelle-like polyhedral bodies found in cyanobacteria and many chemoautotrophic bacteria that are thought to facilitate carbon fixation. Carboxysomes are bounded by a proteinaceous outer shell and filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the first enzyme in the CO2 fixation pathway, but exactly how they enhance carbon fixation is unclear. Here we report the three-dimensional structure of purified carboxysomes from Synechococcus species strain WH8102 as revealed by electron cryotomography. We found that while the sizes of individual carboxysomes in this organism varied from 114 to 137 nm, surprisingly, all were approximately icosahedral. There were on average ∼250 RuBisCOs per carboxysome, organized into 3-4 concentric layers. Some models of carboxysome function depend on specific contacts between individual RuBisCOs and the shell, but no evidence of such contacts was found: no systematic patterns of connecting densities or RuBisCO positions against the shell's presumed hexagonal lattice could be discerned, and simulations showed that packing forces alone could account for the layered organization of RuBisCOs. PMID:17669419

The origin of life and its methodological challenge.

PubMed

Wächtershäuser, G

1997-08-21

The problem of the origin of life is discussed from a methodological point of view as an encounter between the teleological thinking of the historian and the mechanistic thinking of the chemist; and as the Kantian task of replacing teleology by mechanism. It is shown how the Popperian situational logic of historic understanding and the Popperian principle of explanatory power of scientific theories, when jointly applied to biochemistry, lead to a methodology of biochemical retrodiction, whereby common precursor functions are constructed for disparate successor functions. This methodology is exemplified by central tenets of the theory of the chemo-autotrophic origin of life: the proposal of a surface metabolism with a two-dimensional order; the basic polarity of life with negatively charged constituents on positively charged mineral surfaces; the surface-metabolic origin of phosphorylated sugar metabolism and nucleic acids; the origin of membrane lipids and of chemi-osmosis on pyrite surfaces; and the principles of the origin of the genetic machinery. The theory presents the early evolution of life as a process that begins with chemical necessity and winds up in genetic chance.

Resource utilization and trophic position of nematodes and harpacticoid copepods in and adjacent to Zostera noltii beds

NASA Astrophysics Data System (ADS)

Vafeiadou, A.-M.; Materatski, P.; Adão, H.; De Troch, M.; Moens, T.

2014-01-01

This study examines the resource use and trophic position of nematodes and harpacticoid copepods at the genus/species level in an estuarine food web in Zostera noltii beds and in adjacent bare sediments, using the natural abundance of stable carbon and nitrogen isotopes. Microphytobenthos is among the main resources of most taxa, but seagrass-associated resources (i.e. seagrass detritus and epiphytes) also contribute to meiobenthos nutrition, with seagrass detritus being available also in deeper sediments and in unvegetated patches close to seagrass beds. A predominant dependence on chemoautotrophic bacteria was demonstrated for the nematode genus Terschellingia and the copepod family Cletodidae. A predatory feeding mode is illustrated for Paracomesoma and other Comesomatidae, which were previously considered first-level consumers (deposit feeders) according to their buccal morphology. The considerable variation found in both resource use and trophic level among nematode genera from the same feeding type, and even among congeneric nematode species, shows that interpretation of nematode feeding ecology based purely on mouth morphology should be avoided.

Resource utilization and trophic position of nematodes and harpacticoid copepods in and adjacent to Zostera noltii beds

NASA Astrophysics Data System (ADS)

Vafeiadou, A.-M.; Materatski, P.; Adão, H.; De Troch, M.; Moens, T.

2014-07-01

This study examines the resource use and trophic position of nematodes and harpacticoid copepods at the genus/species level in an estuarine food web in Zostera noltii beds and in adjacent bare sediments using the natural abundance of stable carbon and nitrogen isotopes. Microphytobenthos and/or epiphytes are among the main resources of most taxa, but seagrass detritus and sediment particulate organic matter contribute as well to meiobenthos nutrition, which are also available in deeper sediment layers and in unvegetated patches close to seagrass beds. A predominant dependence on chemoautotrophic bacteria was demonstrated for the nematode genus Terschellingia and the copepod family Cletodidae. A predatory feeding mode is illustrated for Paracomesoma and other Comesomatidae, which were previously considered first-level consumers (deposit feeders) according to their buccal morphology. The considerable variation found in both resource use and trophic level among nematode genera from the same feeding type, and even among congeneric nematode species, shows that the interpretation of nematode feeding ecology based purely on mouth morphology should be avoided.

A process economic assessment of hydrocarbon biofuels production using chemoautotrophic organisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khan, NE; Myers, JA; Tuerk, AL

Economic analysis of an ARPA-e Electrofuels (http://arpa-e.energy.gov/?q=arpa-e-programs/electrofuels) process is presented, utilizing metabolically engineered Rhodobacter capsulatus or Ralstonia eutropha to produce the C30+ hydrocarbon fuel, botryococcene, from hydrogen, carbon dioxide, and oxygen. The analysis is based on an Aspen plus (R) bioreactor model taking into account experimentally determined Rba. capsulatus and Rls. eutropha growth and maintenance requirements, reactor residence time, correlations for gas-liquid mass-transfer coefficient, gas composition, and specific cellular fuel productivity. Based on reactor simulation results encompassing technically relevant parameter ranges, the capital and operating costs of the process were estimated for 5000 bbl-fuel/day plant and used to predict fuelmore » cost. Under the assumptions used in this analysis and crude oil prices, the Levelized Cost of Electricity (LCOE) required for economic feasibility must be less than 2(sic)/kWh. While not feasible under current market prices and costs, this work identifies key variables impacting process cost and discusses potential alternative paths toward economic feasibility. (C) 2014 Elsevier Ltd. All rights reserved.« less

Extraction of extracellular lipids from chemoautotrophic bacteria Serratia sp. ISTD04 for production of biodiesel.

PubMed

Bharti, Randhir K; Srivastava, Shaili; Thakur, Indu Shekhar

2014-08-01

A CO2 sequestering bacterial strain, Serratia sp. ISTD04, that produces a significant amount of extracellular lipids was isolated from marble mine rocks. (14)C labeling analysis revealed that the rate of assimilation of CO2 by the strain is 0.756×10(-9)μmolCO2fixedcell(-1)h(-1). It was found to produce 466mg/l of extracellular lipid which was characterized using (1)H NMR. After transesterification of lipids, the total saturated and unsaturated FAME was found to be 51% and 49% respectively. The major FAME contained in the biodiesel were palmitic acid methyl ester (C16:0), oleic acid methyl ester (C18:1) and 10-nonadecenoic acid methyl ester (C19:1). Biodiesel produced by Serratia sp. ISTD04 is balanced in terms of FAME composition of good quality. It also contained higher proportion of oleic acid (35%) which makes it suitable for utilization in existing engines. Thus, the strain can be harnessed commercially to sequester CO2 into biodiesel. Copyright © 2014 Elsevier Ltd. All rights reserved.

The origin of intermediary metabolism

NASA Technical Reports Server (NTRS)

Morowitz, H. J.; Kostelnik, J. D.; Yang, J.; Cody, G. D.

2000-01-01

The core of intermediary metabolism in autotrophs is the citric acid cycle. In a certain group of chemoautotrophs, the reductive citric acid cycle is an engine of synthesis, taking in CO(2) and synthesizing the molecules of the cycle. We have examined the chemistry of a model system of C, H, and O that starts with carbon dioxide and reductants and uses redox couples as the energy source. To inquire into the reaction networks that might emerge, we start with the largest available database of organic molecules, Beilstein on-line, and prune by a set of physical and chemical constraints applicable to the model system. From the 3.5 million entries in Beilstein we emerge with 153 molecules that contain all 11 members of the reductive citric acid cycle. A small number of selection rules generates a very constrained subset, suggesting that this is the type of reaction model that will prove useful in the study of biogenesis. The model indicates that the metabolism shown in the universal chart of pathways may be central to the origin of life, is emergent from organic chemistry, and may be unique.

Predictive isotopic biogeochemistry: hydrocarbons from anoxic marine basins

NASA Technical Reports Server (NTRS)

Freeman, K. H.; Wakeham, S. G.; Hayes, J. M.

1994-01-01

Carbon isotopic compositions were determined for individual hydrocarbons in water column and sediment samples from the Cariaco Trench and Black Sea. In order to identify hydrocarbons derived from phytoplankton, the isotopic compositions expected for biomass of autotrophic organisms living in surface waters of both localities were calculated based on the concentrations of CO2(aq) and the isotopic compositions of dissolved inorganic carbon. These calculated values are compared to measured delta values for particulate organic carbon and for individual hydrocarbon compounds. Specifically, we find that lycopane is probably derived from phytoplankton and that diploptene is derived from the lipids of chemoautotrophs living above the oxic/anoxic boundary. Three acyclic isoprenoids that have been considered markers for methanogens, pentamethyleicosane and two hydrogenated squalenes, have different delta values and apparently do not derive from a common source. Based on the concentration profiles and isotopic compositions, the C31 and C33 n-alkanes and n-alkenes have a similar source, and both may have a planktonic origin. If so, previously assigned terrestrial origins of organic matter in some Black Sea sediments may be erroneous.

The Biological Deep Sea Hydrothermal Vent as a Model to Study Carbon Dioxide Capturing Enzymes

PubMed Central

Minic, Zoran; Thongbam, Premila D.

2011-01-01

Deep sea hydrothermal vents are located along the mid-ocean ridge system, near volcanically active areas, where tectonic plates are moving away from each other. Sea water penetrates the fissures of the volcanic bed and is heated by magma. This heated sea water rises to the surface dissolving large amounts of minerals which provide a source of energy and nutrients to chemoautotrophic organisms. Although this environment is characterized by extreme conditions (high temperature, high pressure, chemical toxicity, acidic pH and absence of photosynthesis) a diversity of microorganisms and many animal species are specially adapted to this hostile environment. These organisms have developed a very efficient metabolism for the assimilation of inorganic CO2 from the external environment. In order to develop technology for the capture of carbon dioxide to reduce greenhouse gases in the atmosphere, enzymes involved in CO2 fixation and assimilation might be very useful. This review describes some current research concerning CO2 fixation and assimilation in the deep sea environment and possible biotechnological application of enzymes for carbon dioxide capture. PMID:21673885

Denitrifying SUP05 Require Exogenous Nitrogen

NASA Astrophysics Data System (ADS)

Shah, V.; Chang, B. X.; Morris, R. M.

2016-02-01

Members of the SUP05 clade of gamma-proteobacteria are among the most abundant chemoautotrophs in the ocean. Environmental sequencing studies suggest that they have critical roles in mediating carbon fixation, denitrification, and sulfur oxidation in oxygen minimum zones (OMZs). They have evaded cultivation and little is known about the specific growth requirements or substrate ranges that determine their abundance, distribution and impact on marine biogeochemical cycles. We evaluated the genetic potential of an isolate from the SUP05 clade "Ca. Thioglobus autotrophica strain EF1" to fix carbon, reduce nitrogen and oxidize sulfur under anaerobic growth conditions. Growth experiments support genomic predictions, indicating that strain EF1 is a facultatively anaerobic sulfur-oxidizing chemolithoautotroph that reduces nitrate to nitrite and nitric oxide to nitrous oxide. These experiments also revealed that strain EF1 is limited for growth by ammonium, which indicates that it requires an exogenous source of nitrogen for biosynthesis. Evidence that SUP05 cells produce nitrite and nitrous oxide and require exogenous nitrogen suggests that they have important roles in nitrogen cycling and that their growth is ultimately limited by the degradation of sinking organic matter.

New insights into hydrothermal vent processes in the unique shallow-submarine arc-volcano, Kolumbo (Santorini), Greece

PubMed Central

Kilias, Stephanos P.; Nomikou, Paraskevi; Papanikolaou, Dimitrios; Polymenakou, Paraskevi N.; Godelitsas, Athanasios; Argyraki, Ariadne; Carey, Steven; Gamaletsos, Platon; Mertzimekis, Theo J.; Stathopoulou, Eleni; Goettlicher, Joerg; Steininger, Ralph; Betzelou, Konstantina; Livanos, Isidoros; Christakis, Christos; Bell, Katherine Croff; Scoullos, Michael

2013-01-01

We report on integrated geomorphological, mineralogical, geochemical and biological investigations of the hydrothermal vent field located on the floor of the density-stratified acidic (pH ~ 5) crater of the Kolumbo shallow-submarine arc-volcano, near Santorini. Kolumbo features rare geodynamic setting at convergent boundaries, where arc-volcanism and seafloor hydrothermal activity are occurring in thinned continental crust. Special focus is given to unique enrichments of polymetallic spires in Sb and Tl (±Hg, As, Au, Ag, Zn) indicating a new hybrid seafloor analogue of epithermal-to-volcanic-hosted-massive-sulphide deposits. Iron microbial-mat analyses reveal dominating ferrihydrite-type phases, and high-proportion of microbial sequences akin to "Nitrosopumilus maritimus", a mesophilic Thaumarchaeota strain capable of chemoautotrophic growth on hydrothermal ammonia and CO2. Our findings highlight that acidic shallow-submarine hydrothermal vents nourish marine ecosystems in which nitrifying Archaea are important and suggest ferrihydrite-type Fe3+-(hydrated)-oxyhydroxides in associated low-temperature iron mats are formed by anaerobic Fe2+-oxidation, dependent on microbially produced nitrate. PMID:23939372

Sulphur isotopic compositions of deep-sea hydrothermal vent animals

NASA Technical Reports Server (NTRS)

Fry, B.; Gest, H.; Hayes, J. M.

1983-01-01

The S-34/S-32 ratios of tissues from vestimentiferan worms, brachyuran crabs, and giant clams living around deep hydrothermal vents are reported. Clean tissues were dried, ground, suspended in 0.1 M LiCl, shaken twice at 37 C to remove seawater sulfates, dried at 60 C, combusted in O2 in a Parr bomb. Sulfur was recovered as BaSO4, and the isotopic abundances in SO2 generated by thermal decomposition of 5-30-mg samples were determined using an isotope-ratio mass spectrometer. The results are expressed as delta S-34 and compared with values measured in seawater sulfates and in normal marine fauna. The values ranged from -4.7 to 4.7 per thousand, comparable to vent sulfide minerals (1.3-4.1 per thousand) and distinct from seawater sulfates (20.1 per thousand) and normal marine fauna (about 13-20 per thousand). These results indicate that vent sulfur rather than seawater sulfur is utilized by these animals, a process probably mediated by chemoautotrophic bacteria which can use inorganic sulfur compounds as energy sources.

The biological deep sea hydrothermal vent as a model to study carbon dioxide capturing enzymes.

PubMed

Minic, Zoran; Thongbam, Premila D

2011-01-01

Deep sea hydrothermal vents are located along the mid-ocean ridge system, near volcanically active areas, where tectonic plates are moving away from each other. Sea water penetrates the fissures of the volcanic bed and is heated by magma. This heated sea water rises to the surface dissolving large amounts of minerals which provide a source of energy and nutrients to chemoautotrophic organisms. Although this environment is characterized by extreme conditions (high temperature, high pressure, chemical toxicity, acidic pH and absence of photosynthesis) a diversity of microorganisms and many animal species are specially adapted to this hostile environment. These organisms have developed a very efficient metabolism for the assimilation of inorganic CO₂ from the external environment. In order to develop technology for the capture of carbon dioxide to reduce greenhouse gases in the atmosphere, enzymes involved in CO₂ fixation and assimilation might be very useful. This review describes some current research concerning CO₂ fixation and assimilation in the deep sea environment and possible biotechnological application of enzymes for carbon dioxide capture.

Can the hemoglobin characteristics of vesicomyid clam species influence their distribution in deep-sea sulfide-rich sediments? A case study in the Angola Basin

NASA Astrophysics Data System (ADS)

Decker, C.; Zorn, N.; Le Bruchec, J.; Caprais, J. C.; Potier, N.; Leize-Wagner, E.; Lallier, F. H.; Olu, K.; Andersen, A. C.

2017-08-01

Vesicomyids live in endosymbiosis with sulfur-oxidizing bacteria and therefore need hydrogen sulfide to survive. They can nevertheless live in a wide range of sulfide and oxygen levels and depths, which may explain the exceptional diversity of this clam family in deep-sea habitats. In the Gulf of Guinea, nine species of vesicomyid clams are known to live in cold-seep areas with pockmarks from 600 to 3200 m deep, as well as in the organic-rich sediments of the Congo deep-sea fan at 5000 m deep. Our previous study showed that two species living in a giant pockmark have different oxygen carriers, suggesting different adaptations to hypoxia. Here, we studied the hemoglobin structure and oxygen affinity in three other species, Calyptogena valdiviae, Elenaconcha guiness and Abyssogena southwardae to determine whether the characteristics of their oxygen carriers contribute to their distribution in sulfide-rich sediments at a regional scale. Documenting pairwise species associations in various proportions, we give a semi-quantitative account of their local distribution and oxygen and sulfide measurements at seven sites. Mass spectrometry showed that each vesicomyid species has four intracellular monomeric hemoglobin molecules of 15-16 kDa, all differing in their molecular mass. As expected, the monomers showed no cooperativity in oxygen binding. Their oxygen affinities were very high (below 1 Torr), but differed significantly. C. valdiviae had the highest affinity and was dominant in the Harp pockmark, the site with the lowest oxygen content (half the value of fully oxygenated water). A. southwardae dominated in the Congo Lobe area, the site with the deepest sulfides. We discuss how hemoglobin may favor an active, vertical distribution of vesicomyids in sulfide-rich sediments.

Microbially mediated carbon cycling at the Cenomanian-Turonian transition in lacustrine environments

NASA Astrophysics Data System (ADS)

Wu, H.; Zhang, S.; Jiang, G.; Underwood, M.; Wan, X.

2009-12-01

The Late Cretaceous Cenomanian-Turonian (C-T) transition records a major ocean anoxic event (OAE2) and a positive carbon isotope excursion. These events have been documented mostly from marine successions and their expression in terrestrial environments is highly desirable. Here we report a high-resolution organic carbon isotope record across the C-T boundary from the Qingshankou Formation (K2qn) of the terrestrial Songliao Basin (SLB) in northeastern China. Samples were collected from the drilled core (SK-1) and cover the bottom 60 m of the K2qn that has been correlated to the C-T transition using the astronomical time scale. The results show a long-term negative δ13Corg excursion superimposed on short-term δ13Corg cycles. Most δ13Corg cycles have a reverse relationship with total organic carbon (TOC) concentration, except at the beginning and the end of the long-term δ13Corg excursion. Spectral analysis of the δ13Corg, TOC and Gamma Ray Logging curves (GR) reveals three distinct cycle bands with the thickness of 14.5-9.0m, 5.8-3.4m and 2.2-1.5m, which were interpreted as the short eccentricity, obliquity, and precession cycles, respectively. The investigated section recorded about 7 short eccentricity and 39 precession cycles. The reverse relationship between TOC and δ13Corg is inconsistent with the general TOC-δ13Corg pattern seen in most lacustrine environments, in which increasing primary productivity (and thus TOC) in the epilimnion results in higher δ13Corg values. In combination with existing biomarker data from K2qn, the TOC-δ13Corg pattern in SLB is better explained by microbially mediated carbon cycling that is astronomically controlled by the precession cycles. During precession minima (summer insolation maxima) periods, intensified precipitation and increased chemical weathering may have led to sustained eutrophication in SLB and the bloom of chemoautotrophic and methanotrophic organisms in the basin. Significant biomass contribution from chemoautotrophic and methanotrophic organisms resulted in lower δ13Corg values. During precession maximum, seasonal changes and reduced nutrient supply kept better water circulation and a lower chemocline. Most organic carbon contribution was from photosynthetic organisms and has relatively higher δ13Corg values. The positive TOC-δ13Corg correlation at the beginning and end of the long-term negative δ13Corg excursion can be interpreted as resulting from the algal/diatom blooms at the onset and ending of the eccentricity cycle, during which high surface water production and a lower chemocline were maintained. The data indicate sustained anoxia/euxinia in the SLB during the time of OAE2, suggesting a paleoclimate event influencing both the marine and terrestrial systems.

Functional Metagenomic Investigations of Microbial Communities in a Shallow-Sea Hydrothermal System

PubMed Central

Tang, Kai; Liu, Keshao; Jiao, Nianzhi; Zhang, Yao; Chen, Chen-Tung Arthur

2013-01-01

Little is known about the functional capability of microbial communities in shallow-sea hydrothermal systems (water depth of <200 m). This study analyzed two high-throughput pyrosequencing metagenomic datasets from the vent and the surface water in the shallow-sea hydrothermal system offshore NE Taiwan. This system exhibited distinct geochemical parameters. Metagenomic data revealed that the vent and the surface water were predominated by Epsilonproteobacteria (Nautiliales-like organisms) and Gammaproteobacteria ( Thiomicrospira -like organisms), respectively. A significant difference in microbial carbon fixation and sulfur metabolism was found between the vent and the surface water. The chemoautotrophic microorganisms in the vent and in the surface water might possess the reverse tricarboxylic acid cycle and the Calvin−Bassham−Benson cycle for carbon fixation in response to carbon dioxide highly enriched in the environment, which is possibly fueled by geochemical energy with sulfur and hydrogen. Comparative analyses of metagenomes showed that the shallow-sea metagenomes contained some genes similar to those present in other extreme environments. This study may serve as a basis for deeply understanding the genetic network and functional capability of the microbial members of shallow-sea hydrothermal systems. PMID:23940820

Cold-seep ostracods from the western Svalbard margin: direct palaeo-indicator for methane seepage?

NASA Astrophysics Data System (ADS)

Yasuhara, Moriaki; Sztybor, Kamila; Rasmussen, Tine L.; Okahashi, Hisayo; Sato, Runa; Tanaka, Hayato

2018-01-01

Despite their high abundance and diversity, microfossil taxa adapted to a particular chemosynthetic environment have rarely been studied and are therefore poorly known. Here we report on an ostracod species, Rosaliella svalbardensis gen. et sp. nov., from a cold methane seep site at the western Svalbard margin, Fram Strait. The new species shows a distinct morphology, different from other eucytherurine ostracod genera. It has a marked similarity to Xylocythere, an ostracod genus known from chemosynthetic environments of wood falls and hydrothermal vents. Rosaliella svalbardensis is probably an endemic species or genus linked to methane seeps. We speculate that the surface ornamentation of pore clusters, secondary reticulation, and pit clusters may be related to ectosymbiosis with chemoautotrophic bacteria. This new discovery of specialized microfossil taxa is important because they can be used as an indicator species for past and present seep environments (http://zoobank.org/urn:lsid:zoobank.org:pub:6075FF30-29D5-4DAB-9141-AE722CD3A69B).

Environmental microbes can speciate and cycle arsenic.

PubMed

Rhine, E Danielle; Garcia-Dominguez, Elizabeth; Phelps, Craig D; Young, L Y

2005-12-15

Naturally occurring arsenic is found predominantly as arsenate [As(V)] or arsenite [As(III)], and can be readily oxidized or reduced by microorganisms. Given the health risks associated with arsenic in groundwater and the interest in arsenic-active microorganisms, we hypothesized that environmental microorganisms could mediate a redox cycling of arsenic that is linked to their metabolism. This hypothesis was tested using an As(V) respiring reducer (strain Y5) and an aerobic chemoautotrophic As(II) oxidizer (strain OL1 ) both isolated from a Superfund site, Onondaga Lake, in Syracuse, NY. Strains were grown separately and together in sealed serum bottles, and the oxic/anoxic condition was the only parameter changed. Initially, under anoxic conditions when both isolates were grown together, 2 mM As(V) was stoichiometrically reduced to As(III) within 14 days. Following complete reduction, sterile ambient air was added and within 24 h As(III) was completely oxidized to As(V). The anoxic-oxic cycle was repeated, and sterile controls showed no abiotic transformation within the 28-day incubation period. These results demonstrate that microorganisms can cycle arsenic in response to dynamic environmental conditions, thereby affecting the speciation, and hence mobility and toxicity of arsenic in the environment.

Shallow stratification prevailed for ∼1700 to ∼1300 Ma ocean: Evidence from organic carbon isotopes in the North China Craton

NASA Astrophysics Data System (ADS)

Luo, Genming; Junium, Christopher K.; Kump, Lee R.; Huang, Junhua; Li, Chao; Feng, Qinglai; Shi, Xiaoying; Bai, Xiao; Xie, Shucheng

2014-08-01

The Late Paleoproterozoic to Early Mesoproterozoic (from ∼1700 Ma to ∼1300 Ma) was highlighted by the assembly of the Nuna supercontinent, expansion of euxinic marine environments and apparent stasis in the diversity of eukaryotes. The isotopic composition of carbonate carbon (δ13Ccarb) was surprisingly constant during this interval, but little is known about the secular variation in the organic carbon isotopic composition (δ13Corg). Here we report δ13Corg data from the latest Paleoproterozoic (>1650 Ma) to Early Mesoproterozoic (∼1300 Ma) succession in North China. The δ13Corg values range from -25‰ to -34‰, and are dependent on sedimentary facies. In subtidal and deeper environments δ13Corg values are low and constant, ca. -32‰, but relatively enriched and more variable in shallower intertidal and supratidal environments. We attribute the facies-dependent variation in δ13Corg to the presence of a shallow chemocline. A probable result of a shallow chemocline is that it supported significant contributions of organic matter produced by chemoautotrophic and/or anaerobic photoautotrophic microbes in relatively deep environments from the latest Paleoproterozoic to Early Mesoproterozoic continental shelf of North China.

The microbial arsenic cycle in Mono Lake, California

USGS Publications Warehouse

Oremland, Ronald S.; Stolz, John F.; Hollibaugh, James T.

2004-01-01

Significant concentrations of dissolved inorganic arsenic can be found in the waters of a number of lakes located in the western USA and in other water bodies around the world. These lakes are often situated in arid, volcanic terrain. The highest concentrations of arsenic occur in hypersaline, closed basin soda lakes and their remnant brines. Although arsenic is a well-known toxicant to eukaryotes and prokaryotes alike, some prokaryotes have evolved biochemical mechanisms to exploit arsenic oxyanions (i.e., arsenate and arsenite); they can use them either as an electron acceptor for anaerobic respiration (arsenate), or as an electron donor (arsenite) to support chemoautotrophic fixation of CO2 into cell carbon. Unlike in freshwater or marine ecosystems, these processes may assume quantitative significance with respect to the carbon cycle in arsenic-rich soda lakes. For the past several years our research has focused on the occurrence and biogeochemical manifestations of these processes in Mono Lake, a particularly arsenic-rich environment. Herein we review some of our findings concerning the biogeochemical arsenic cycle in this lake, with the hope that it may broaden the understanding of the influence of microorganisms upon the speciation of arsenic in more common, less “extreme” environments, such as drinking water aquifers.

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi

PubMed Central

Numoto, Nobutaka; Nakagawa, Taro; Kita, Akiko; Sasayama, Yuichi; Fukumori, Yoshihiro; Miki, Kunio

2005-01-01

Mouthless and gutless marine animals, pogonophorans and vestimentiferans, obtain their nutrition solely from their symbiotic chemoautotrophic sulfur-oxidizing bacteria. These animals have sulfide-binding 400-kDa and/or 3,500-kDa Hb, which transports oxygen and sulfide simultaneously. The symbiotic bacteria are supplied with sulfide by Hb of the host animal and use it to provide carbon compounds. Here, we report the crystal structure of a 400-kDa Hb from pogonophoran Oligobrachia mashikoi at 2.85-Å resolution. The structure is hollow-spherical, composed of a total of 24 globins as a dimer of dodecamer. This dodecameric assemblage would be a fundamental structural unit of both 400-kDa and 3,500-kDa Hbs. The structure of the mercury derivative used for phasing provides insights into the sulfide-binding mechanism. The mercury compounds bound to all free Cys residues that have been expected as sulfide-binding sites. Some of the free Cys residues are surrounded by Phe aromatic rings, and mercury atoms come into contact with these residues in the derivative structure. It is strongly suggested that sulfur atoms bound to these sites could be stabilized by aromatic-electrostatic interactions by the surrounding Phe residues. PMID:16204001

Deep-biosphere consortium of fungi and prokaryotes in Eocene subseafloor basalts.

PubMed

Bengtson, S; Ivarsson, M; Astolfo, A; Belivanova, V; Broman, C; Marone, F; Stampanoni, M

2014-11-01

The deep biosphere of the subseafloor crust is believed to contain a significant part of Earth's biomass, but because of the difficulties of directly observing the living organisms, its composition and ecology are poorly known. We report here a consortium of fossilized prokaryotic and eukaryotic micro-organisms, occupying cavities in deep-drilled vesicular basalt from the Emperor Seamounts, Pacific Ocean, 67.5 m below seafloor (mbsf). Fungal hyphae provide the framework on which prokaryote-like organisms are suspended like cobwebs and iron-oxidizing bacteria form microstromatolites (Frutexites). The spatial inter-relationships show that the organisms were living at the same time in an integrated fashion, suggesting symbiotic interdependence. The community is contemporaneous with secondary mineralizations of calcite partly filling the cavities. The fungal hyphae frequently extend into the calcite, indicating that they were able to bore into the substrate through mineral dissolution. A symbiotic relationship with chemoautotrophs, as inferred for the observed consortium, may be a pre-requisite for the eukaryotic colonization of crustal rocks. Fossils thus open a window to the extant as well as the ancient deep biosphere. © 2014 The Authors. Geobiology Published by John Wiley & Sons Ltd.

Conifer Growth Response to Snowpack across an Elevation Gradient in Northern Sierra Nevada Mountains, California

NASA Astrophysics Data System (ADS)

Lepley, K. S.; Touchan, R.; Meko, D. M.; Graham, R.; Shamir, E.

2016-12-01

The United States depends heavily on the agricultural resources of the state of California, and water is the key factor in sustaining these resources. Around a third of the state's water supply originates from snow in the Sierra Nevada Mountains. Managing this resource demands understanding of climatic variability on time-scales of decades to centuries to plan for drought conditions in the region. Tree-ring growth spanning several centuries can serve as proxy records and provide the knowledge upon which to base sound decisions for water-resource management. Here we will discuss the growth-response of six tree species to April 1st snow-water equivalent (SWE) across an elevation gradient of 1500 m to 2525 m. Higher elevation (ca. 1890 m to 2525 m) tree-ring chronologies exhibit significant correlation (r = 0.45 to r = 0.57, p < 0.01) with April 1st SWE during the 20th century. Abies magnifica (ABMA), Tsuga mertensiana, and Calocedrus decurrens exhibit a positive response to prior-year snowpack, while Abies concolor responds positively to same-year snowpack. Lower elevation Pinus ponderosa (PIPO) and Juniperus occidentalis chronologies show no significant correlation with SWE, however PIPO responds positively at a site 500 m higher in elevation. In contrast, ABMA chronologies from two sites with a 500 m elevation difference exhibit the same response to snowpack. The strong relationship between annual tree-ring growth and April 1st SWE in these tree species opens possibilities of exploring historic snowpack patterns and elucidating dendroclimatic relationships in the mountainous west.

Examining the diversity and distribution of microbial communities from newly discovered methane seeps along the Cascadia Margin

NASA Astrophysics Data System (ADS)

Seabrook, S.; Thurber, A. R.; Embley, R. W.; Raineault, N.; Baumberger, T.; Merle, S. G.

2016-12-01

Methane seeps provide biogeochemical and microbial heterogeneity in deep-sea habitats. In June of 2016 the E/V Nautilus, exploring for methane seeps along the Cascadia continental margin, discovered over 450 bubble streams, indicative of active seepage, and collected biological samples at 6 of the resulting newly discovered seeps. These seeps covered a range of depths, latitudes, habitat types and biogeochemical environments and included: Juan de Fuca (150m), Astoria canyon (800m and 500m), Nehalem Bank (185m), Heceta SW (1200m), SW Coquille Bank (600m), and Klamath Knoll seep (700m). Geologic environment types included continental shelf, canyons and slopes, and these sites spanned the zone of hydrate stability and the Oxygen Minimum Zone. A range of seep-specific habitat were found and sampled including: reduced sediments, microbial mats, methane hydrates, clam beds (Calyptogena spp.), Siboglinidae tubeworm assemblages and sparse assemblages of stalked barnacles. Here, we present an initial characterization of the microbial communities collected via push cores by a remotely operated vehicle (ROV) at the six aforementioned sites. With high throughput amplicon sequencing of the V4-V5 region of the 16S rRNA gene, we characterize the diversity and microbial composition of the seep sites sampled. This characterization is furthered with digital drop PCR of the pmoA gene (involved with aerobic methanotrophy) to allow for a comparison of the community composition with functional gene abundance of critical microbial processes. These data will be placed in the greater biogeochemical context of the region, including direct comparison with paired gas-tight sampling at key locations. The results of these analyses will provide the first microbial description of this broad range of seep ecosystems along the Cascadia Margin adding to our overall understanding of microbial diversity, the dominant physiological processes at seep ecosystems, and the connection between community structure, function and biogeochemistry in habitats which we are just starting to appreciate for their ubiquity in marine environments.

Transcriptional Response of the Archaeal Ammonia Oxidizer Nitrosopumilus maritimus to Low and Environmentally Relevant Ammonia Concentrations

PubMed Central

Stahl, David A.

2013-01-01

The ability of chemoautotrophic ammonia-oxidizing archaea to compete for ammonia among marine microorganisms at low ambient concentrations has been in part attributed to their extremely high affinity for ammonia, but as yet there is no mechanistic understanding of supporting metabolism. We examined transcription of selected genes for anabolic functions (CO2 fixation, ammonia transport, and cell wall synthesis) and a central catabolic function (ammonia oxidation) in the thaumarchaeon Nitrosopumilus maritimus SCM1 growing at two ammonia concentrations, as measured by combined ammonia and ammonium, one well above the Km for ammonia oxidation (∼500 μM) and the other well below the Km (<10 nM). Transcript levels were generally immediately and differentially repressed when cells transitioned from ammonia-replete to ammonia-limiting conditions. Transcript levels for ammonia oxidation, CO2 fixation, and one of the ammonia transport genes were approximately the same at high and low ammonia availability. Transcripts for all analyzed genes decreased with time in the complete absence of ammonia, but with various rates of decay. The new steady-state mRNA levels established are presumably more reflective of the natural physiological state of ammonia-oxidizing archaea and offer a reference for interpreting message abundance patterns in the natural environment. PMID:23995944

Carbon isotopes in biological carbonates: Respiration and photosynthesis

USGS Publications Warehouse

McConnaughey, T.A.; Burdett, J.; Whelan, J.F.; Paull, C.K.

1997-01-01

Respired carbon dioxide is an important constituent in the carbonates of most air breathing animals but is much less important in the carbonates of most aquatic animals. This difference is illustrated using carbon isotope data from freshwater and terrestrial snails, ahermatypic corals, and chemoautotrophic and methanotrophic pelecypods. Literature data from fish otoliths and bird and mammal shell and bone carbonates are also considered. Environmental CO2/O2 ratios appear to be the major controlling variable. Atmospheric CO2/O2 ratios are about thirty times lower than in most natural waters, hence air breathing animals absorb less environmental CO2 in the course of obtaining O2. Tissue CO2 therefore, does not isotopically equilibrate with environmental CO2 as thoroughly in air breathers as in aquatic animals, and this is reflected in skeletal carbonates. Animals having efficient oxygen transport systems, such as vertebrates, also accumulate more respired CO2 in their tissues. Photosynthetic corals calcify mainly during the daytime when photosynthetic CO2 uptake is several times faster than respiratory CO2 release. Photosynthesis, therefore, affects skeletal ??13C more strongly than does respiration. Corals also illustrate how "metabolic" effects on skeletal isotopic composition can be estimated, despite the presence of much larger "kinetic" isotope effects. Copyright ?? 1997 Elsevier Science Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kreel, Nathan E.; Tabita, F. Robert; Berg, Ivan

Archaeal ribulose 1, 5-bisphospate carboxylase/oxygenase (RubisCO) is differentiated from other RubisCO enzymes and is classified as a form III enzyme, as opposed to the form I and form II RubisCOs typical of chemoautotrophic bacteria and prokaryotic and eukaryotic phototrophs. The form III enzyme from archaea is particularly interesting as several of these proteins exhibit unusual and reversible sensitivity to molecular oxygen, including the enzyme from Archaeoglobus fulgidus. Previous studies with A. fulgidus RbcL2 had shown the importance of Met-295 in oxygen sensitivity and pointed towards the potential significance of another residue (Ser-363) found in a hydrophobic pocket that is conservedmore » in all RubisCO proteins. In the current study, further structure/function studies have been performed focusing on Ser-363 of A. fulgidus RbcL2; various changes in this and other residues of the hydrophobic pocket point to and definitively establish the importance of Ser-363 with respect to interactions with oxygen. In addition, previous findings had indicated discrepant CO 2/O 2 specificity determinations of the Thermococcus kodakaraensis RubisCO, a close homolog of A. fulgidus RbcL2. As a result, it is shown here that the T. kodakaraensis enzyme exhibits a similar substrate specificity as the A. fulgidus enzyme and is also oxygen sensitive, with equivalent residues involved in oxygen interactions.« less

Trophosome of the Deep-Sea Tubeworm Riftia pachyptila Inhibits Bacterial Growth.

PubMed

Klose, Julia; Aistleitner, Karin; Horn, Matthias; Krenn, Liselotte; Dirsch, Verena; Zehl, Martin; Bright, Monika

2016-01-01

The giant tubeworm Riftia pachyptila lives in symbiosis with the chemoautotrophic gammaproteobacterium Cand. Endoriftia persephone. Symbionts are released back into the environment upon host death in high-pressure experiments, while microbial fouling is not involved in trophosome degradation. Therefore, we examined the antimicrobial effect of the tubeworm's trophosome and skin. The growth of all four tested Gram-positive, but only of one of the tested Gram-negative bacterial strains was inhibited by freshly fixed and degrading trophosome (incubated up to ten days at either warm or cold temperature), while no effect on Saccharomyces cerevisiae was observed. The skin did not show antimicrobial effects. A liquid chromatography-mass spectrometric analysis of the ethanol supernatant of fixed trophosomes lead to the tentative identification of the phospholipids 1-palmitoleyl-2-lyso-phosphatidylethanolamine, 2-palmitoleyl-1-lyso-phosphatidylethanolamine and the free fatty acids palmitoleic, palmitic and oleic acid, which are known to have an antimicrobial effect. As a result of tissue autolysis, the abundance of the free fatty acids increased with longer incubation time of trophosome samples. This correlated with an increasing growth inhibition of Bacillus subtilis and Listeria welshimeri, but not of the other bacterial strains. Therefore, the free fatty acids produced upon host degradation could be the cause of inhibition of at least these two bacterial strains.

The vent microbiome: patterns and drivers

NASA Astrophysics Data System (ADS)

Pachiadaki, M.

2015-12-01

Microbial processes within deep-sea hydrothermal vents affect the global biogeochemical cycles. Still, there are significant gaps in our understanding of the microbiology and the biogeochemistry of deep-sea hydrothermal systems. Vents differ in temperature, host rock composition and fluid chemistry; factors that are hypothesized to shape the distribution of the microbial communities, their metabolic capabilities and their activities. Using large-scale single cell genomics, we obtained insights into the genomic content of several linkages of a diffuse flow vent. The genomes show high metabolic versatility. Sulfur oxidation appears to be predominant but there is the potential of using a variety of e- donors and acceptors to obtain energy. To further assess the ecological importance of the vent auto- and heterotrophs, the global biogeography of the analyzed lineages will be investigated by fragment recruitment of metagenomes produced from the same site as well as other hydrothermal systems. Metatranscriptomic and metaproteomic data will be integrated to examine the expression of the predominant metabolic pathways and thus the main energy sources driving chemoautotrophic production. The comparative analysis of the key players and associated pathways among various vent sites that differ in physicochemical characteristics is anticipated to decipher the patterns and drivers of the global dispersion and the local diversification of the vent microbiome.

Polymersomes containing iron sulfide (FeS) as primordial cell model : for the investigation of energy providing redox reactions.

PubMed

Alpermann, Theodor; Rüdel, Kristin; Rüger, Ronny; Steiniger, Frank; Nietzsche, Sandor; Filiz, Volkan; Förster, Stephan; Fahr, Alfred; Weigand, Wolfgang

2011-04-01

According to Wächtershäuser's "Iron-Sulfur-World" one major requirement for the development of life on the prebiotic Earth is compartmentalization. Vesicles spontaneously formed from amphiphilic components containing a specific set of molecules including sulfide minerals may have lead to the first autotrophic prebiotic units. The iron sulfide minerals may have been formed by geological conversions in the environment of deep-sea volcanos (black smokers), which can be observed even today. Wächtershäuser postulated the evolution of chemical pathways as fundamentals of the origin of life on earth. In contrast to the classical Miller-Urey experiment, depending on external energy sources, the "Iron-Sulfur-World" is based on the catalytic and energy reproducing redox system FeS+H2S-->FeS2+H2. The energy release out of this redox reaction (∆RG°=-38 kJ/mol, pH 0) could be the cause for the subsequent synthesis of complex organic molecules and the precondition for the development of more complex units similar to cells known today. Here we show the possibility for precipitating iron sulfide inside vesicles composed of amphiphilic block-copolymers as a model system for a first prebiotic unit. Our findings could be an indication for a chemoautotrophic FeS based origin of life.

Respiration Strategies Utilized by the Gill Endosymbiont from the Host Lucinid Codakia orbicularis (Bivalvia: Lucinidae)

PubMed Central

Duplessis, Melinda R.; Ziebis, Wiebke; Gros, Olivier; Caro, Audrey; Robidart, Julie; Felbeck, Horst

2004-01-01

The large tropical lucinid clam Codakia orbicularis has a symbiotic relationship with intracellular, sulfide-oxidizing chemoautotrophic bacteria. The respiration strategies utilized by the symbiont were explored using integrative techniques on mechanically purified symbionts and intact clam-symbiont associations along with habitat analysis. Previous work on a related symbiont species found in the host lucinid Lucinoma aequizonata showed that the symbionts obligately used nitrate as an electron acceptor, even under oxygenated conditions. In contrast, the symbionts of C. orbicularis use oxygen as the primary electron acceptor while evidence for nitrate respiration was lacking. Direct measurements obtained by using microelectrodes in purified symbiont suspensions showed that the symbionts consumed oxygen; this intracellular respiration was confirmed by using the redox dye CTC (5-cyano-2,3-ditolyl tetrazolium chloride). In the few intact chemosymbioses tested in previous studies, hydrogen sulfide production was shown to occur when the animal-symbiont association was exposed to anoxia and elemental sulfur stored in the thioautotrophic symbionts was proposed to serve as an electron sink in the absence of oxygen and nitrate. However, this is the first study to show by direct measurements using sulfide microelectrodes in enriched symbiont suspensions that the symbionts are the actual source of sulfide under anoxic conditions. PMID:15240294

Automatic content-based analysis of georeferenced image data: Detection of Beggiatoa mats in seafloor video mosaics from the HÅkon Mosby Mud Volcano

NASA Astrophysics Data System (ADS)

Jerosch, K.; Lüdtke, A.; Schlüter, M.; Ioannidis, G. T.

2007-02-01

The combination of new underwater technology as remotely operating vehicles (ROVs), high-resolution video imagery, and software to compute georeferenced mosaics of the seafloor provides new opportunities for marine geological or biological studies and applications in offshore industry. Even during single surveys by ROVs or towed systems large amounts of images are compiled. While these underwater techniques are now well-engineered, there is still a lack of methods for the automatic analysis of the acquired image data. During ROV dives more than 4200 georeferenced video mosaics were compiled for the HÅkon Mosby Mud Volcano (HMMV). Mud volcanoes as HMMV are considered as significant source locations for methane characterised by unique chemoautotrophic communities as Beggiatoa mats. For the detection and quantification of the spatial distribution of Beggiatoa mats an automated image analysis technique was developed, which applies watershed transformation and relaxation-based labelling of pre-segmented regions. Comparison of the data derived by visual inspection of 2840 video images with the automated image analysis revealed similarities with a precision better than 90%. We consider this as a step towards a time-efficient and accurate analysis of seafloor images for computation of geochemical budgets and identification of habitats at the seafloor.

Early Evolution of Earth's Geochemical Cycle and Biosphere: Implications for Mars Exobiology

NASA Technical Reports Server (NTRS)

DesMarais, David J.; Chang, Sherwood (Technical Monitor)

1997-01-01

Carbon (C) has played multiple key roles for life and its environment. C has formed organics, greenhouse gases, aquatic pH buffers, redox buffers, and magmatic constituents affecting plutonism and volcanism. These roles interacted across a network of reservoirs and processes known as the biogeochemical C cycle. Changes in the cycle over geologic time were driven by increasing solar luminosity, declining planetary heat flow, and continental and biological evolution. The early Archean C cycle was dominated by hydrothermal alteration of crustal rocks and by thermal emanations of CO2 and reduced species (eg., H2, Fe(2+) and sulfides). Bioorganic synthesis was achieved by nonphotosynthetic CO2-fixing bacteria (chemoautotrophs) and, possibly, bacteria (organotrophs) utilizing any available nonbiological organic C. Responding both to abundant solar energy and to a longterm decline in thermal sources of chemical energy and reducing power, the blaspheme first developed anoxygenic photosynthesis, then, ultimately, oxygenic photosynthesis. O2-photosynthesis played a central role in transforming the ancient environment and blaspheme to the modem world. The geochemical C cycles of early Earth and Mars were quite similar. The principal differences between the modem C cycles of these planets arose during the later evolution of their heat flows, crusts, atmospheres and, perhaps, their blasphemes.

Major role of microbes in carbon fluxes during Austral winter in the Southern Drake Passage.

PubMed

Manganelli, Maura; Malfatti, Francesca; Samo, Ty J; Mitchell, B Greg; Wang, Haili; Azam, Farooq

2009-09-14

Carbon cycling in Southern Ocean is a major issue in climate change, hence the need to understand the role of biota in the regulation of carbon fixation and cycling. Southern Ocean is a heterogeneous system, characterized by a strong seasonality, due to long dark winter. Yet, currently little is known about biogeochemical dynamics during this season, particularly in the deeper part of the ocean. We studied bacterial communities and processes in summer and winter cruises in the southern Drake Passage. Here we show that in winter, when the primary production is greatly reduced, Bacteria and Archaea become the major producers of biogenic particles, at the expense of dissolved organic carbon drawdown. Heterotrophic production and chemoautotrophic CO(2) fixation rates were substantial, also in deep water, and bacterial populations were controlled by protists and viruses. A dynamic food web is also consistent with the observed temporal and spatial variations in archaeal and bacterial communities that might exploit various niches. Thus, Southern Ocean microbial loop may substantially maintain a wintertime food web and system respiration at the expense of summer produced DOC as well as regenerate nutrients and iron. Our findings have important implications for Southern Ocean ecosystem functioning and carbon cycle and its manipulation by iron enrichment to achieve net sequestration of atmospheric CO(2).

Microbial diversity in nonsulfur, sulfur and iron geothermal steam vents.

PubMed

Benson, Courtney A; Bizzoco, Richard W; Lipson, David A; Kelley, Scott T

2011-04-01

Fumaroles, commonly called steam vents, are ubiquitous features of geothermal habitats. Recent studies have discovered microorganisms in condensed fumarole steam, but fumarole deposits have proven refractory to DNA isolation. In this study, we report the development of novel DNA isolation approaches for fumarole deposit microbial community analysis. Deposit samples were collected from steam vents and caves in Hawaii Volcanoes National Park, Yellowstone National Park and Lassen Volcanic National Park. Samples were analyzed by X-ray microanalysis and classified as nonsulfur, sulfur or iron-dominated steam deposits. We experienced considerable difficulty in obtaining high-yield, high-quality DNA for cloning: only half of all the samples ultimately yielded sequences. Analysis of archaeal 16S rRNA gene sequences showed that sulfur steam deposits were dominated by Sulfolobus and Acidianus, while nonsulfur deposits contained mainly unknown Crenarchaeota. Several of these novel Crenarchaeota lineages were related to chemoautotrophic ammonia oxidizers, indicating that fumaroles represent a putative habitat for ammonia-oxidizing Archaea. We also generated archaeal and bacterial enrichment cultures from the majority of the deposits and isolated members of the Sulfolobales. Our results provide the first evidence of Archaea in geothermal steam deposits and show that fumaroles harbor diverse and novel microbial lineages. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Stepwise Evolution of Nonliving to Living Chemical Systems

NASA Astrophysics Data System (ADS)

Lindahl, Paul A.

2004-08-01

Steps by which a nonliving chemical system could have transformed into a living system are described and discussed, assuming general features of Wächtershäuser's chemo-autotrophic surface theory of the origin of life. Environmental species such as CO2 and H2S are proposed to have reacted to form a quasi-steady state metal-bound intermediate (CH3-M) that slowly decayed into waste (CH4). Unpredictable dispersive reactions expanded the system to include surface-bound forms of the citric acid cycle intermediates (oxaloacetate --> citrate). Further reaction yielded an autocatalytic system in which raw materials are converted into the system at exponential rates. Combinatorial dispersive reactions that improved the performance of this system were automatically selected and incorporated into it. Systems evolved critical features of living systems (proteins, membranes, proteins, nucleic acids, etc.) using two related mechanisms called grafting and waste-conversion. Such living systems were transformed from less recognizable types (characterized by autocatalytic spreading, decentralization, poorly defined boundaries, etc.) into more recognizable ones (encapsulated by membranes, controlled by single-molecule genomes, etc.) that self-replicated by a cell division cycle and could evolve by the standard gene-based Darwinian mechanism. The resulting systems are viewed as having an autocatalytic network composed of three linked autocatalytic subreactions.

Carbon isotopes in biological carbonates: Respiration and photosynthesis

NASA Astrophysics Data System (ADS)

McConnaughey, Ted A.; Burdett, Jim; Whelan, Joseph F.; Paull, Charles K.

1997-02-01

Respired carbon dioxide is an important constituent in the carbonates of most air breathing animals but is much less important in the carbonates of most aquatic animals. This difference is illustrated using carbon isotope data from freshwater and terrestrial snails, ahermatypic corals, and chemoautotrophic and methanotrophic pelecypods. Literature data from fish otoliths and bird and mammal shell and bone carbonates are also considered. Environmental CO 2/O 2 ratios appear to be the major controlling variable. Atmospheric CO 2/O 2 ratios are about thirty times lower than in most natural waters, hence air breathing animals absorb less environmental CO 2 in the course of obtaining 0 2. Tissue CO 2 therefore, does not isotopically equilibrate with environmental CO 2 as thoroughly in air breathers as in aquatic animals, and this is reflected in skeletal carbonates. Animals having efficient oxygen transport systems, such as vertebrates, also accumulate more respired CO 2 in their tissues. Photosynthetic corals calcify mainly during the daytime when photosynthetic CO 2 uptake is several times faster than respiratory CO 2 release. Photosynthesis, therefore, affects skeletal δ13C more strongly than does respiration. Corals also illustrate how "metabolic" effects on skeletal isotopic composition can be estimated, despite the presence of much larger "kinetic" isotope effects.

Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile

USGS Publications Warehouse

Neilson, Julia W.; Quade, Jay; Ortiz, Marianyoly; Nelson, William M.; Legatzki, Antje; Tian, Fei; LaComb, Michelle; Betancourt, Julio L.; Wing, Rod A.; Soderlund, Carol A.; Maier, Raina M.

2012-01-01

Nearly half the earth's surface is occupied by dryland ecosystems, regions susceptible to reduced states of biological productivity caused by climate fluctuations. Of these regions, arid zones located at the interface between vegetated semiarid regions and biologically unproductive hyperarid zones are considered most vulnerable. The objective of this study was to conduct a deep diversity analysis of bacterial communities in unvegetated arid soils of the Atacama Desert, to characterize community structure and infer the functional potential of these communities based on observed phylogenetic associations. A 454-pyrotag analysis was conducted of three unvegetated arid sites located at the hyperarid-arid margin. The analysis revealed communities with unique bacterial diversity marked by high abundances of novel Actinobacteria and Chloroflexi and low levels of Acidobacteria and Proteobacteria, phyla that are dominant in many biomes. A 16S rRNA gene library of one site revealed the presence of clones with phylogenetic associations to chemoautotrophic taxa able to obtain energy through oxidation of nitrite, carbon monoxide, iron, or sulfur. Thus, soils at the hyperarid margin were found to harbor a wealth of novel bacteria and to support potentially viable communities with phylogenetic associations to non-phototrophic primary producers and bacteria capable of biogeochemical cycling.

A Search for Life in the Subsurface At Rio Tinto Spain, An Analog To Searching For Life On Mars.

NASA Astrophysics Data System (ADS)

Stoker, C. R.

2003-12-01

Most familiar life forms on Earth live in the surface biosphere where liquid water, sunlight, and the essential chemical elements for life are abundant. However, such environments are not found on Mars or anywhere else in the solar system. On Mars, the surface environmental conditions of pressure and temperature prevent formation of liquid water. Furthermore, conditions at the Martian surface are unfavorable to life due to intense ultraviolet radiation and strong oxidizing compounds that destroy organic compounds. However, subsurface liquid water on Mars has been predicted on theoretical grounds. The recent discovery of near surface ground ice by the Mars Odyssey mission, and the abundant evidence for recent Gully features observed by the Mars Global Surveyor mission strengthen the case for subsurface liquid water on Mars. Thus, the strategy for searching for life on Mars points to drilling to the depth of liquid water, bringing samples to the surface and analyzing them with instrumentation to detect in situ organisms and biomarker compounds. The MARTE (Mars Astrobiology Research and Technology Experiment) project is a field experiment focused on searching for a hypothesized subsurface anaerobic chemoautotrophic biosphere in the region of the Rio Tinto, a river in southwestern Spain while also demonstrating technology relevant to searching for a subsurface biosphere on Mars. The Tinto river is located in the Iberian Pyrite belt, one of the largest deposits of sulfide minerals in the world. The surface (river) system is an acidic extreme environment produced and maintained by microbes that metabolize sulfide minerals and produce sulfuric acid as a byproduct. Evidence suggests that the river is a surface manifestation of an underground biochemical reactor. Organisms found in the river are capable of chemoautotrophic metabolism using sulfide and ferric iron mineral substrates, suggesting these organisms could thrive in groundwater which is the source of the Rio Tinto. The MARTE project will simulate the search for subsurface life on Mars using a drilling system developed for future Mars flight to accomplish subsurface access. Augmenting the drill are robotic systems for extracting the cores from the drill head and performing analysis using a suite of instruments to understand the composition, mineralogy, presence of organics, and to search for life signatures in subsurface samples. A robotic bore-hole inspection system will characterize borehole properties in situ. A Mars drilling mission simulation including remote operation of the drilling, sample handling, and instruments and interpretation of results by a remote science team will be performed. This simulated mission will be augmented by manual methods of drilling, sample handling, and sample analysis to fully document the subsurface, prevent surface microbial contamination, identify subsurface biota, and compare what can be learned with robotically-operated instruments. The first drilling campaign in the MARTE project takes place in September 2003 and is focused on characterizing the microbiology of the subsurface at Rio Tinto using conventional drilling, sample handling and laboratory analysis techniques. Lessons learned from this "ground truth" drilling campaign will guide the development of robotic systems and instruments needed for searching for life underground on Mars.

Yeast identification in floral nectar of Mimulus aurantiacus (Invited)

NASA Astrophysics Data System (ADS)

Kyauk, C.; Belisle, M.; Fukami, T.

2009-12-01

Nectar is such a sugar-rich resource that serves as a natural habitat in which microbes thrive. As a result, yeasts arrive to nectar on the bodies of pollinators such as hummingbirds and bees. Yeasts use the sugar in nectar for their own needs when introduced. This research focuses on the identification of different types of yeast that are found in the nectar of Mimulus aurantiacus (commonly known as sticky monkey-flower). Unopened Mimulus aurantiacus flower buds were tagged at Jasper Ridge and bagged three days later. Floral nectar was then extracted and plated on potato dextrose agar. Colonies on the plates were isolated and DNA was extracted from each sample using QIAGEN DNeasy Plant Mini Kit. The DNA was amplified through PCR and ran through gel electrophoresis. The PCR product was used to clone the nectar samples into an E.coli vector. Finally, a phylogenetic tree was created by BLAST searching sequences in GenBank using the Internal Transcribed Space (ITS) locus. It was found that 18 of the 50 identified species were Candida magnifica, 14 was Candida rancensis, 6 were Crytococcus albidus and there were 3 or less of the following: Starmella bombicola, Candida floricola, Aureobasidium pullulans, Pichia kluyvera, Metschnikowa cibodaserisis, Rhodotorua colostri, and Malassezia globosa. The low diversity of the yeast could have been due to several factors: time of collection, demographics of Jasper Ridge, low variety of pollinators, and sugar concentration of the nectar. The results of this study serve as a necessary first step for a recently started research project on ecological interactions between plants, pollinators, and nectar-living yeast. More generally, this research studies the use of the nectar-living yeast community as a natural microcosm for addressing basic questions about the role of dispersal and competitive and facilitative interactions in ecological succession.

Spatial patterns of large natural fires in Sierra Nevada wilderness areas

USGS Publications Warehouse

Collins, B.M.; Kelly, M.; van Wagtendonk, J.W.; Stephens, S.L.

2007-01-01

The effects of fire on vegetation vary based on the properties and amount of existing biomass (or fuel) in a forest stand, weather conditions, and topography. Identifying controls over the spatial patterning of fire-induced vegetation change, or fire severity, is critical in understanding fire as a landscape scale process. We use gridded estimates of fire severity, derived from Landsat ETM+ imagery, to identify the biotic and abiotic factors contributing to the observed spatial patterns of fire severity in two large natural fires. Regression tree analysis indicates the importance of weather, topography, and vegetation variables in explaining fire severity patterns between the two fires. Relative humidity explained the highest proportion of total sum of squares throughout the Hoover fire (Yosemite National Park, 2001). The lowest fire severity corresponded with increased relative humidity. For the Williams fire (Sequoia/Kings Canyon National Parks, 2003) dominant vegetation type explains the highest proportion of sum of squares. Dominant vegetation was also important in determining fire severity throughout the Hoover fire. In both fires, forest stands that were dominated by lodgepole pine (Pinus contorta) burned at highest severity, while red fir (Abies magnifica) stands corresponded with the lowest fire severities. There was evidence in both fires that lower wind speed corresponded with higher fire severity, although the highest fire severity in the Williams fire occurred during increased wind speed. Additionally, in the vegetation types that were associated with lower severity, burn severity was lowest when the time since last fire was fewer than 11 and 17 years for the Williams and Hoover fires, respectively. Based on the factors and patterns identified, managers can anticipate the effects of management ignited and naturally ignited fires at the forest stand and the landscape levels. ?? 2007 Springer Science+Business Media, Inc.

Reconstructing the muscular ground pattern of phylactolaemate bryozoans: first data from gelatinous representatives.

PubMed

Gawin, Natalie; Wanninger, Andreas; Schwaha, Thomas

2017-11-07

Phylactolaemata is commonly regarded the earliest branch within Bryozoa and thus the sister group to the other bryozoan taxa, Cyclostomata and Gymnolaemata. Therefore, the taxon is important for the reconstruction of the bryozoan morphological ground pattern. In this study the myoanatomy of Pectinatella magnifica, Cristatella mucedo and Hyalinella punctata was analysed by means of histology, f-actin staining and confocal laser-scanning microscopy in order to fill gaps in knowledge concerning the myoanatomy of Phylactolaemata. The retractor muscles and muscles of the aperture, gut, body wall, tentacle sheath, lophophore constitute the most prominent muscular subsets in these species. The lophophore shows longitudinal muscle bands in the tentacles, lophophoral arm muscles, epistome musculature and hitherto undescribed muscles of the ring canal. In general the muscular system of the three species is very similar with differences mainly in the body wall, tentacle sheath and epistome. The body wall contains an orthogonal grid of musculature. The epistome exhibits either a muscular meshwork in the epistomal wall or muscle fibers traversing the epistomal cavity. The whole tentacle sheath possesses a regular mesh of muscles in Pectinatella and Cristatella, whereas circular muscles are limited to the tentacle sheath base in Hyalinella. This study is the first to describe muscles of the ring canal and contributes to reconstructing muscular features for the last common ancestor of all bryozoans. The data available suggest that two longitudinal muscle bands in the tentacles, as well as retractor muscles and longitudinal and circular muscles in the tentacle sheath, were present in the last common bryozoan ancestor. Comparisons among bryozoans shows that several apomorphies are present in the myoanatomy of each class- level taxon such as the epistomal musculature and musculature of the lophophoral arms in phylactolaemates, annular muscles in cyclostomes and parietal muscles in gymnolaemates.

High-Elevation Sierra Nevada Conifers Reveal Increasing Reliance on Snow Water with Changing Climate

NASA Astrophysics Data System (ADS)

Lepley, K. S.; Meko, D. M.; Touchan, R.; Shamir, E.; Graham, R.

2017-12-01

Snowpack in the Sierra Nevada Mountains accounts for around one third of California's water supply. Melting snow can provide water into dry summer months characteristic of the region's Mediterranean climate. As climate changes, understanding patterns of snowpack, snowmelt, and biological response are critical in this region of agricultural, recreational, and ecological value. Tree rings can act as proxy records to inform scientists and resource managers of past climate variability where instrumental data is unavailable. Here we investigate relationships between tree rings of high-elevation, snow-adapted conifer trees (Tsuga mertensiana, Abies magnifica) and April 1st snow-water equivalent (SWE) in the northern Sierra Nevada Mountains. The 1st principal component of 29 highly correlated regional SWE time series was modeled using multiple linear regression of four tree-ring chronologies including two lagged chronologies. Split-period verification analysis of this model revealed poor predictive skill in the early half (1929 - 1966) of the calibration period (1929 - 2003). Further analysis revealed a significant (p < 0.01) change in correlation between the Tsuga mertensiana chronology and SWE during early (1929 - 1970) and late (1971 - 2013) periods. Running 31-year correlations between this chronology and SWE rose from r = 0.10 in 1950 to r = 0.77 in 1996. This strengthening relationship is coincident with a positive trend in temperature, a negative trend in SWE, and increased variability in precipitation through time. Snow water is becoming a more limiting resource to tree growth as average temperatures rise and the hydrologic regime shifts. These results highlight the need for resource managers and policy makers to consider that biological response to climate is not static.

Carbon Source Preference in Chemosynthetic Hot Spring Communities

PubMed Central

Urschel, Matthew R.; Kubo, Michael D.; Hoehler, Tori M.; Peters, John W.

2015-01-01

Rates of dissolved inorganic carbon (DIC), formate, and acetate mineralization and/or assimilation were determined in 13 high-temperature (>73°C) hot springs in Yellowstone National Park (YNP), Wyoming, in order to evaluate the relative importance of these substrates in supporting microbial metabolism. While 9 of the hot spring communities exhibited rates of DIC assimilation that were greater than those of formate and acetate assimilation, 2 exhibited rates of formate and/or acetate assimilation that exceeded those of DIC assimilation. Overall rates of DIC, formate, and acetate mineralization and assimilation were positively correlated with spring pH but showed little correlation with temperature. Communities sampled from hot springs with similar geochemistries generally exhibited similar rates of substrate transformation, as well as similar community compositions, as revealed by 16S rRNA gene-tagged sequencing. Amendment of microcosms with small (micromolar) amounts of formate suppressed DIC assimilation in short-term (<45-min) incubations, despite the presence of native DIC concentrations that exceeded those of added formate by 2 to 3 orders of magnitude. The concentration of added formate required to suppress DIC assimilation was similar to the affinity constant (Km) for formate transformation, as determined by community kinetic assays. These results suggest that dominant chemoautotrophs in high-temperature communities are facultatively autotrophic or mixotrophic, are adapted to fluctuating nutrient availabilities, and are capable of taking advantage of energy-rich organic substrates when they become available. PMID:25819970

Anaerobic chemolithotrophic growth of the haloalkaliphilic bacterium strain MLMS‑1 by disproportionation of monothioarsenate

USGS Publications Warehouse

Planer-Friedrich, B.; Hartig, C.; Lohmayer, R.; Suess, E.; McCann, Shelley; Oremland, Ronald S.

2015-01-01

A novel chemolithotrophic metabolism based on a mixed arsenic−sulfur species has been discovered for the anaerobic deltaproteobacterium, strain MLMS-1, a haloalkaliphile isolated from Mono Lake, California, U.S. Strain MLMS‑1 is the first reported obligate arsenate-respiring chemoautotroph which grows by coupling arsenate reduction to arsenite with the oxidation of sulfide to sulfate. In that pathway the formation of a mixed arsenic−sulfur species was reported. That species was assumed to be monothioarsenite ([H2AsIIIS−IIO2] −), formed as an intermediate by abiotic reaction of arsenite with sulfide. We now report that this species is monothioarsenate ([HAsVS−IIO3] 2−) as revealed by X-ray absorption spectroscopy. Monothioarsenate forms by abiotic reaction of arsenite with zerovalent sulfur. Monothioarsenate is kinetically stable under a wide range of pH and redox conditions. However, it was metabolized rapidly by strain MLMS-1 when incubated with arsenate. Incubations using monothioarsenate confirmed that strain MLMS-1 was able to grow (μ = 0.017 h−1 ) on this substrate via a disproportionation reaction by oxidizing the thio-group-sulfur (S−II) to zerovalent sulfur or sulfate while concurrently reducing the central arsenic atom (AsV) to arsenite. Monothioarsenate disproportionation could be widespread in nature beyond the already studied arsenic and sulfide rich hot springs and soda lakes where it was discovered.

A paradox resolved: Sulfide acquisition by roots of seep tubeworms sustains net chemoautotrophy

PubMed Central

Freytag, John K.; Girguis, Peter R.; Bergquist, Derk C.; Andras, Jason P.; Childress, James J.; Fisher, Charles R.

2001-01-01

Vestimentiferan tubeworms, symbiotic with sulfur-oxidizing chemoautotrophic bacteria, dominate many cold-seep sites in the Gulf of Mexico. The most abundant vestimentiferan species at these sites, Lamellibrachia cf. luymesi, grows quite slowly to lengths exceeding 2 meters and lives in excess of 170–250 years. L. cf. luymesi can grow a posterior extension of its tube and tissue, termed a “root,” down into sulfidic sediments below its point of original attachment. This extension can be longer than the anterior portion of the animal. Here we show, using methods optimized for detection of hydrogen sulfide down to 0.1 μM in seawater, that hydrogen sulfide was never detected around the plumes of large cold-seep vestimentiferans and rarely detectable only around the bases of mature aggregations. Respiration experiments, which exposed the root portions of L. cf. luymesi to sulfide concentrations between 51–561 μM, demonstrate that L. cf. luymesi use their roots as a respiratory surface to acquire sulfide at an average rate of 4.1 μmol⋅g−1⋅h−1. Net dissolved inorganic carbon uptake across the plume of the tubeworms was shown to occur in response to exposure of the posterior (root) portion of the worms to sulfide, demonstrating that sulfide acquisition by roots of the seep vestimentiferan L. cf. luymesi can be sufficient to fuel net autotrophic total dissolved inorganic carbon uptake. PMID:11687647

Simultaneous treatment of dimethyl disulfide and hydrogen sulfide in an alkaline biotrickling filter.

PubMed

Arellano-García, Luis; Le Borgne, Sylvie; Revah, Sergio

2018-01-01

Foul odors comprise generally a complex mixture of molecules, where reduced sulfur compounds play a key role due to their toxicity and low odor threshold. Previous reports on treating mixtures of sulfur compounds in single biofilters showed that hydrogen sulfide (H 2 S) interferes with the removal and degradation of other sulfur compounds. In this study, hydrogen sulfide (H 2 S) and dimethyl disulfide (DMDS) were fed to an alkaline biotrickling filter (ABTF) at pH 10, to evaluate the simultaneous removal of inorganic and organic sulfur compounds in a single, basic-pH system. The H 2 S-DMDS mixture was treated for more than 200 days, with a gas residence time of 40 s, attaining elimination capacities of 86 g DMDS m -3 h -1 and 17 g H2S m -3 h -1 and removal efficiencies close to 100%. Conversion of H 2 S and DMDS to sulfate was generally above 70%. Consumption of sulfide and formaldehyde was verified by respirometry, suggesting the coexistence of both methylotrophic and chemoautotrophic breakdown pathways by the immobilized alkaliphilic biomass. The molecular biology analysis showed that the long-term acclimation of the ABTF led to a great variety of bacteria, predominated by Thioalkalivibrio species, while fungal community was notoriously less diverse and dominated by Fusarium species. Copyright © 2017. Published by Elsevier Ltd.

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

DOE PAGES

Jungbluth, Sean P.; Glavina del Rio, Tijana; Tringe, Susannah G.; ...

2017-04-06

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “more » Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “ Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Finally, our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.« less

Food-web structure of seep sediment macrobenthos from the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Demopoulos, Amanda W. J.; Gualtieri, Daniel; Kovacs, Kaitlin

2010-11-01

The slope environment of the Gulf of Mexico (GOM) supports dense communities of seep megafaunal invertebrates that rely on endosymbiotic bacteria for nutrition. Seep sediments also contain smaller macrofaunal invertebrates whose nutritional pathways are not well understood. Using stable-isotope analysis, we investigate the utilization of chemosynthetically fixed and methane-derived organic matter by macrofauna. Biological sampling was conducted in three lower-slope GOM seep environs: Green Canyon (GC852, 1428 m), Atwater Valley (AT340, 2230 m), and Alaminos Canyon (AC601, 2384 m). Infaunal δ13C and δ15N exhibited a broad range of values; most infauna appeared to be heterotrophic, although several taxa had very light δ15N and δ13C values, indicating possible reliance on chemoautotrophic symbioses. The lightest δ13C and δ15N values were observed in nematodes (δ13C=-54.6±0.1‰, δ15N=-6.1±0.2‰) and one gastropod (δ13C=-54.1‰, δ15N=-1.1‰) from Green Canyon. Mixing-model results indicated that sulfur-oxidizing Beggiatoa may be an important food source for seep infauna; the rate of utilization ranged from 60% to 100% at Green Canyon and Atwater Valley. The overall range in isotope values was similar across the three sites, suggesting that biogeochemical processes may be very similar in these geographically distinct areas.

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jungbluth, Sean P.; Glavina del Rio, Tijana; Tringe, Susannah G.

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “more » Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “ Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Finally, our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.« less

Shifts in the meso- and bathypelagic archaea communities composition during recovery and short-term handling of decompressed deep-sea samples.

PubMed

La Cono, Violetta; Smedile, Francesco; La Spada, Gina; Arcadi, Erika; Genovese, Maria; Ruggeri, Gioacchino; Genovese, Lucrezia; Giuliano, Laura; Yakimov, Michail M

2015-06-01

Dark ocean microbial communities are actively involved in chemoautotrophic and anaplerotic fixation of bicarbonate. Thus, aphotic pelagic realm of the ocean might represent a significant sink of CO2 and source of primary production. However, the estimated metabolic activities in the dark ocean are fraught with uncertainties. Typically, deep-sea samples are recovered to the sea surface for downstream processing on deck. Shifts in ambient settings, associated with such treatments, can likely change the metabolic activity and community structure of deep-sea adapted autochthonous microbial populations. To estimate influence of recovery and short-term handling of deep-sea samples, we monitored the succession of bathypelagic microbial community during its 3 days long on deck incubation. We demonstrated that at the end of exposition, the deep-sea archaeal population decreased threefold, whereas the bacterial fraction doubled in size. As revealed by phylogenetic analyses of amoA gene transcripts, dominance of the active ammonium-oxidizing bathypelagic Thaumarchaeota groups shifted over time very fast. These findings demonstrated the simultaneous existence of various 'deep-sea ecotypes', differentially reacting to the sampling and downstream handling. Our study supports the hypothesis that metabolically active members of meso- and bathypelagic Thaumarchaeota possess the habitat-specific distribution, metabolic complexity and genetic divergence at subpopulation level. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

PubMed Central

Glavina del Rio, Tijana; Tringe, Susannah G.; Stepanauskas, Ramunas

2017-01-01

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments. PMID:28396823

DNA-SIP Reveals the Diversity of Chemolithoautotrophic Bacteria Inhabiting Three Different Soil Types in Typical Karst Rocky Desertification Ecosystems in Southwest China.

PubMed

Li, Baoqin; Li, Zhe; Sun, Xiaoxu; Wang, Qi; Xiao, Enzong; Sun, Weimin

2018-05-04

Autotrophs that inhabit soils receive less attention than their counterparts in other ecosystems, such as deep-sea and subsurface sediments, due to the low abundance of autotrophs in soils with high organic contents. However, the karst rocky desertification region is a unique ecosystem that may have a low level of organic compounds. Therefore, we propose that karst rocky desertification ecosystems may harbor diverse autotrophic microbial communities. In this study, DNA-SIP was employed to identify the chemolithoautotrophic bacteria inhabiting three soil types (i.e., grass, forest, and agriculture) of the karst rocky desertification ecosystems. The results indicated that potential chemolithoautotrophic population was observed in each soil type, even at different time points after amending 13 C-NaHCO 3 , confirming our hypothesis that diverse autotrophs contribute to the carbon cycle in karst soils. Bacteria, such as Ralstonia, Ochrobactrum, Brevibacterium, Acinetobacter, and Corynebacterium, demonstrated their potential to assimilate inorganic carbon and reduce nitrate or thiosulfate as electron acceptors. Putative mixotrophs were identified by DNA-SIP as well, suggesting the metabolic versatility of soil microbiota. A co-occurrence network further indicated that autotrophs and heterotrophs may form associated communities to sustain the ecosystem function. Our current study revealed the metabolic diversity of autotrophic bacteria in soil habitats and demonstrated the potentially important role of chemoautotrophs in karst rocky desertification ecosystems.

Nitrogen Fixation in Thermophilic Chemosynthetic Microbial Communities Depending on Hydrogen, Sulfate, and Carbon Dioxide

PubMed Central

Nishihara, Arisa; Haruta, Shin; McGlynn, Shawn E.; Thiel, Vera; Matsuura, Katsumi

2018-01-01

The activity of nitrogen fixation measured by acetylene reduction was examined in chemosynthetic microbial mats at 72–75°C in slightly-alkaline sulfidic hot springs in Nakabusa, Japan. Nitrogenase activity markedly varied from sampling to sampling. Nitrogenase activity did not correlate with methane production, but was detected in samples showing methane production levels less than the maximum amount, indicating a possible redox dependency of nitrogenase activity. Nitrogenase activity was not affected by 2-bromo-ethane sulfonate, an inhibitor of methanogenesis. However, it was inhibited by the addition of molybdate, an inhibitor of sulfate reduction and sulfur disproportionation, suggesting the involvement of sulfate-reducing or sulfur-disproportionating organisms. Nitrogenase activity was affected by different O2 concentrations in the gas phase, again supporting the hypothesis of a redox potential dependency, and was decreased by the dispersion of mats with a homogenizer. The loss of activity that occurred from dispersion was partially recovered by the addition of H2, sulfate, and carbon dioxide. These results suggested that the observed activity of nitrogen fixation was related to chemoautotrophic sulfate reducers, and fixation may be active in a limited range of ambient redox potential. Since thermophilic chemosynthetic communities may resemble ancient microbial communities before the appearance of photosynthesis, the present results may be useful when considering the ancient nitrogen cycle on earth. PMID:29367473

Comparative metagenomic analysis of the microbial communities in the surroundings of Iheya north and Iheya ridge hydrothermal fields reveals insights into the survival strategy of microorganisms in deep-sea environments

NASA Astrophysics Data System (ADS)

Wang, Hai-liang; Sun, Li

2018-04-01

In this study, metagenomic analysis was performed to investigate the taxonomic compositions and metabolic profiles of the microbial communities inhabiting the sediments in the surroundings of Iheya North and Iheya Ridge hydrothermal fields. The microbial communities in four different samples were found to be dominated by bacteria and, to a much lesser extent, archaea belonging to the phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Deinococcus-Thermus, and Nitrospirae, which play important roles in the cycling of carbon, nitrogen, and sulfur. All four microbial communities (i) contained chemoautotrophs and heterotrophs, the former probably fixed CO2 via various carbon fixation pathways, and the latter may degrade organic matters using nitrate and sulfate as electron acceptors, (ii) exhibited an abundance of DNA repair genes and bacterial sulfur oxidation mediated by reverse sulfate reduction, and (iii) harbored bacteria and archaea involved in anaerobic methane oxidation via intra-aerobic denitrification and reverse methanogenesis, which were found for the first time in hydrothermal areas. Furthermore, genes involved in DNA repair, reductive acetyl-CoA pathway, and ammonia metabolism were possibly affected by distance to the vent fields. These findings facilitate our understanding of the strategies of the microbial communities to adapt to the environments in deep sea areas associated with hydrothermal vents.

From Black Hole to Hydrate Hole: Gas hydrates, authigenic carbonates and vent biota as indicators of fluid migration at pockmark sites of the Northern Congo Fan

NASA Astrophysics Data System (ADS)

Kasten, S.; Schneider, R.; Spiess, V.; Cruise Participants Of M56b

2003-04-01

A recent high-resolution seismic, echosounder and video survey combined with detailed geological and geochemical sampling of pockmark sites on the Northern Congo Fan was carried out with RV Meteor in November/December 2002 in the frame of the project "CONGO" (BMBF/BEO "Geotechnologien"). These investigations revealed the extensive occurrence of surface and sub-surface gas hydrates as well as characteristic features of fluid venting such as clams (Calyptogena), tube worms (Pogonophera) and huge amounts of authigenic carbonates. In a first approach the patchyness in the occurrence of these features was mapped in relation to pockmark structure and seismic reflectors. Detailed sampling of three pockmarks by gravity corer showed that gas hydrates are present at and close to the sediment surface and often occur as several distinct layers and/or veins intercalated with hemipelagic muds. The depth of the upper boundary of these hydrate-bearing sediments increases from the center towards the edge of the pockmark structures. Pore water concentration profiles of sulfate and methane document the process of anaerobic methane oxidation above the hydrate-bearing layers. For those cores which contained several gas hydrate layers preliminary pore water profiles suggest the occurrence of more than one zone of anaerobic methane oxidation. Authigenic carbonates are found in high abundance, irregularly distributed within the pockmarks close to the sediment surface. These carbonates occur in a wide variety with respect to size, shape, structure and mineralogy. Their formation is associated with high amounts of bicarbonate released by the process of anaerobic methane oxidation. In the gravity cores authigenic carbonates are always present above hydrate-bearing sections. However, the quantities and characteristics of these authigenic minerals in relation to venting and microbial activity as well as to gas hydrate dissociation are not clear yet. Unraveling this relationship will be a major target of further investigation. By means of detailed studies of the sedimentary solid-phase, authigenic carbonates, clam layers and molecular biomarkers we will also try to reconstruct the history of venting and the dynamics of gas hydrate formation and decomposition in the Northern Congo fan area.

Expression of genes involved in the uptake of inorganic carbon in the gill of a deep-sea vesicomyid clam harboring intracellular thioautotrophic bacteria.

PubMed

Hongo, Yuki; Ikuta, Tetsuro; Takaki, Yoshihiro; Shimamura, Shigeru; Shigenobu, Shuji; Maruyama, Tadashi; Yoshida, Takao

2016-07-10

Deep-sea vesicomyid clams, including the genus Phreagena (formerly Calyptogena), harbor thioautotrophic bacterial symbionts in the host symbiosome, which consists of cytoplasmic vacuoles in gill epithelial cells called bacteriocytes. The symbiont requires inorganic carbon (Ci), such as CO2, HCO3(-), and CO3(2-), to synthesize organic compounds, which are utilized by the host clam. The dominant Ci in seawater is HCO3(-), which is impermeable to cell membranes. Within the bacteriocyte, cytoplasmic carbonic anhydrase (CA) from the host, which catalyzes the inter-conversion between CO2 and HCO3(-), has been shown to be abundant and is thought to supply intracellular CO2 to symbionts in the symbiosome. However, the mechanism of Ci uptake by the host gill from seawater is poorly understood. To elucidate the influx pathway of Ci into the bacteriocyte, we isolated the genes related to Ci uptake via the pyrosequencing of cDNA from the gill of Phreagena okutanii, and investigated their expression patterns. Using phylogenetic and amino acid sequence analyses, three solute carrier family 4 (SLC4) bicarbonate transporters (slc4co1, slc4co2, and slc4co4) and two membrane-associated CAs (mcaco1 and mcaco2) were identified as candidate genes for Ci uptake. In an in situ hybridization analysis of gill sections, the expression of mcaco1 and mcaco2 was detected in the bacteriocytes and asymbiotic non-ciliated cells, respectively, and the expression of slc4co1 and slc4co2 was detected in the asymbiotic cells, including the intermediate cells of the inner area and the non-ciliated cells of the external area. Although subcellular localizations of the products of these genes have not been fully elucidated, they may play an important role in the uptake of Ci into the bacteriocytes. These findings will improve our understanding of the Ci transport system in the symbiotic relationships of chemosynthetic bivalves. Copyright © 2016 Elsevier B.V. All rights reserved.

An extensive reef system at the Amazon River mouth

PubMed Central

Moura, Rodrigo L.; Amado-Filho, Gilberto M.; Moraes, Fernando C.; Brasileiro, Poliana S.; Salomon, Paulo S.; Mahiques, Michel M.; Bastos, Alex C.; Almeida, Marcelo G.; Silva, Jomar M.; Araujo, Beatriz F.; Brito, Frederico P.; Rangel, Thiago P.; Oliveira, Braulio C. V.; Bahia, Ricardo G.; Paranhos, Rodolfo P.; Dias, Rodolfo J. S.; Siegle, Eduardo; Figueiredo, Alberto G.; Pereira, Renato C.; Leal, Camille V.; Hajdu, Eduardo; Asp, Nils E.; Gregoracci, Gustavo B.; Neumann-Leitão, Sigrid; Yager, Patricia L.; Francini-Filho, Ronaldo B.; Fróes, Adriana; Campeão, Mariana; Silva, Bruno S.; Moreira, Ana P. B.; Oliveira, Louisi; Soares, Ana C.; Araujo, Lais; Oliveira, Nara L.; Teixeira, João B.; Valle, Rogerio A. B.; Thompson, Cristiane C.; Rezende, Carlos E.; Thompson, Fabiano L.

2016-01-01

Large rivers create major gaps in reef distribution along tropical shelves. The Amazon River represents 20% of the global riverine discharge to the ocean, generating up to a 1.3 × 106–km2 plume, and extensive muddy bottoms in the equatorial margin of South America. As a result, a wide area of the tropical North Atlantic is heavily affected in terms of salinity, pH, light penetration, and sedimentation. Such unfavorable conditions were thought to imprint a major gap in Western Atlantic reefs. We present an extensive carbonate system off the Amazon mouth, underneath the river plume. Significant carbonate sedimentation occurred during lowstand sea level, and still occurs in the outer shelf, resulting in complex hard-bottom topography. A permanent near-bottom wedge of ocean water, together with the seasonal nature of the plume’s eastward retroflection, conditions the existence of this extensive (~9500 km2) hard-bottom mosaic. The Amazon reefs transition from accretive to erosional structures and encompass extensive rhodolith beds. Carbonate structures function as a connectivity corridor for wide depth–ranging reef-associated species, being heavily colonized by large sponges and other structure-forming filter feeders that dwell under low light and high levels of particulates. The oxycline between the plume and subplume is associated with chemoautotrophic and anaerobic microbial metabolisms. The system described here provides several insights about the responses of tropical reefs to suboptimal and marginal reef-building conditions, which are accelerating worldwide due to global changes. PMID:27152336

Dissimilatory arsenate reduction with sulfide as electron donor: Experiments with Mono Lake water and isolation of strain MLMS-1, a chemoautotrophic arsenate respirer

USGS Publications Warehouse

Hoeft, S.E.; Kulp, T.R.; Stolz, J.F.; Hollibaugh, J.T.; Oremland, R.S.

2004-01-01

Anoxic bottom water from Mono Lake, California, can biologically reduce added arsenate without any addition of electron donors. Of the possible in situ inorganic electron donors present, only sulfide was sufficiently abundant to drive this reaction. We tested the ability of sulfide to serve as an electron donor for arsenate reduction in experiments with lake water. Reduction of arsenate to arsenite occurred simultaneously with the removal of sulfide. No loss of sulfide occurred in controls without arsenate or in sterilized samples containing both arsenate and sulfide. The rate of arsenate reduction in lake water was dependent on the amount of available arsenate. We enriched for a bacterium that could achieve growth with sulfide and arsenate in a defined, mineral medium and purified it by serial dilution. The isolate, strain MLMS-1, is a gram-negative, motile curved rod that grows by oxidizing sulfide to sulfate while reducing arsenate to arsenite. Chemoautotrophy was confirmed by the incorporation of H14CO3- into dark-incubated cells, but preliminary gene probing tests with primers for ribulose-1,5-biphosphate carboxylase/oxygenase did not yield PCR-amplified products. Alignment of 16S rRNA sequences indicated that strain MLMS-1 was in the ??-Proteobacteria, located near sulfate reducers like Desulfobulbus sp. (88 to 90% similarity) but more closely related (97%) to unidentified sequences amplified previously from Mono Lake. However, strain MLMS-1 does not grow with sulfate as its electron acceptor.

Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Justice, Nicholas B; Pan, Chongle; Mueller, Ryan

Archaea are widely distributed and yet are most often not the most abundant members of microbial communities. Here, we document a transition from Bacteria- to Archaea-dominated communities in microbial biofilms sampled from the Richmond Mine acid mine drainage (AMD) system (pH 1.0,38 C) and in laboratory-cultivated biofilms. This transition occurs when chemoautotrophic microbial communities that develop at the air-solution interface sink to the sediment-solution interface and degrade under microaerobic and anaerobic conditions. The archaea identified in these sunken biofilms are from the class Thermoplasmata, and in some cases, the highly divergent ARMAN nanoarchaeal lineage. In several of the sunken biofilms,more » nanoarchaea comprise 10 to 25% of the community, based on fluorescent in situ hybridization and metagenomic analyses. Comparative community proteomic analyses show a persistence of bacterial proteins in sunken biofilms, but there is clear evidence for amino acid modifications due to acid hydrolysis. Given the low representation of bacterial cells in sunken biofilms based on microscopy, we infer that hydrolysis reflects proteins derived from lysed cells. For archaea, we detected 2,400 distinct proteins, including a subset involved in proteolysis and peptide uptake. Laboratory cultivation experiments using complex carbon substrates demonstrated anaerobic enrichment of Ferroplasma and Aplasma coupled to the reduction of ferric iron. These findings indicate dominance of acidophilic archaea in degrading biofilms and suggest that they play roles in anaerobic nutrient cycling at low pH.« less

Food-web structure of seep sediment macrobenthos from the Gulf of Mexico

USGS Publications Warehouse

Demopoulos, Amanda W.J.; Gualtieri, Daniel; Kovacs, Kaitlin

2010-01-01

The slope environment of the Gulf of Mexico (GOM) supports dense communities of seep megafaunal invertebrates that rely on endosymbiotic bacteria for nutrition. Seep sediments also contain smaller macrofaunal invertebrates whose nutritional pathways are not well understood. Using stable-isotope analysis, we investigate the utilization of chemosynthetically fixed and methane-derived organic matter by macrofauna. Biological sampling was conducted in three lower-slope GOM seep environs: Green Canyon (GC852, 1428 m), Atwater Valley (AT340, 2230 m), and Alaminos Canyon (AC601, 2384 m). Infaunal delta13C and delta15N exhibited a broad range of values; most infauna appeared to be heterotrophic, although several taxa had very light delta15N and delta13C values, indicating possible reliance on chemoautotrophic symbioses. The lightest delta13C and delta15N values were observed in nematodes (delta13C=-54.6 + or - 0.1 per mil, delta15N=-6.1 + or - 0.2 per mil) and one gastropod (delta13C=-54.1 per mil, delta15N=-1.1 per mil) from Green Canyon. Mixing-model results indicated that sulfur-oxidizing Beggiatoa may be an important food source for seep infauna; the rate of utilization ranged from 60% to 100% at Green Canyon and Atwater Valley. The overall range in isotope values was similar across the three sites, suggesting that biogeochemical processes may be very similar in these geographically distinct areas.

Serine 363 of a Hydrophobic Region of Archaeal Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase from Archaeoglobus fulgidus and Thermococcus kodakaraensis Affects CO2/O2 Substrate Specificity and Oxygen Sensitivity.

PubMed

Kreel, Nathan E; Tabita, F Robert

2015-01-01

Archaeal ribulose 1, 5-bisphospate carboxylase/oxygenase (RubisCO) is differentiated from other RubisCO enzymes and is classified as a form III enzyme, as opposed to the form I and form II RubisCOs typical of chemoautotrophic bacteria and prokaryotic and eukaryotic phototrophs. The form III enzyme from archaea is particularly interesting as several of these proteins exhibit unusual and reversible sensitivity to molecular oxygen, including the enzyme from Archaeoglobus fulgidus. Previous studies with A. fulgidus RbcL2 had shown the importance of Met-295 in oxygen sensitivity and pointed towards the potential significance of another residue (Ser-363) found in a hydrophobic pocket that is conserved in all RubisCO proteins. In the current study, further structure/function studies have been performed focusing on Ser-363 of A. fulgidus RbcL2; various changes in this and other residues of the hydrophobic pocket point to and definitively establish the importance of Ser-363 with respect to interactions with oxygen. In addition, previous findings had indicated discrepant CO2/O2 specificity determinations of the Thermococcus kodakaraensis RubisCO, a close homolog of A. fulgidus RbcL2. It is shown here that the T. kodakaraensis enzyme exhibits a similar substrate specificity as the A. fulgidus enzyme and is also oxygen sensitive, with equivalent residues involved in oxygen interactions.

Serine 363 of a Hydrophobic Region of Archaeal Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase from Archaeoglobus fulgidus and Thermococcus kodakaraensis Affects CO2/O2 Substrate Specificity and Oxygen Sensitivity

PubMed Central

Kreel, Nathan E.; Tabita, F. Robert

2015-01-01

Archaeal ribulose 1, 5-bisphospate carboxylase/oxygenase (RubisCO) is differentiated from other RubisCO enzymes and is classified as a form III enzyme, as opposed to the form I and form II RubisCOs typical of chemoautotrophic bacteria and prokaryotic and eukaryotic phototrophs. The form III enzyme from archaea is particularly interesting as several of these proteins exhibit unusual and reversible sensitivity to molecular oxygen, including the enzyme from Archaeoglobus fulgidus. Previous studies with A. fulgidus RbcL2 had shown the importance of Met-295 in oxygen sensitivity and pointed towards the potential significance of another residue (Ser-363) found in a hydrophobic pocket that is conserved in all RubisCO proteins. In the current study, further structure/function studies have been performed focusing on Ser-363 of A. fulgidus RbcL2; various changes in this and other residues of the hydrophobic pocket point to and definitively establish the importance of Ser-363 with respect to interactions with oxygen. In addition, previous findings had indicated discrepant CO2/O2 specificity determinations of the Thermococcus kodakaraensis RubisCO, a close homolog of A. fulgidus RbcL2. It is shown here that the T. kodakaraensis enzyme exhibits a similar substrate specificity as the A. fulgidus enzyme and is also oxygen sensitive, with equivalent residues involved in oxygen interactions. PMID:26381513

Allying with armored snails: the complete genome of gammaproteobacterial endosymbiont.

PubMed

Nakagawa, Satoshi; Shimamura, Shigeru; Takaki, Yoshihiro; Suzuki, Yohey; Murakami, Shun-ichi; Watanabe, Tamaki; Fujiyoshi, So; Mino, Sayaka; Sawabe, Tomoo; Maeda, Takahiro; Makita, Hiroko; Nemoto, Suguru; Nishimura, Shin-Ichiro; Watanabe, Hiromi; Watsuji, Tomo-o; Takai, Ken

2014-01-01

Deep-sea vents harbor dense populations of various animals that have their specific symbiotic bacteria. Scaly-foot gastropods, which are snails with mineralized scales covering the sides of its foot, have a gammaproteobacterial endosymbiont in their enlarged esophageal glands and diverse epibionts on the surface of their scales. In this study, we report the complete genome sequencing of gammaproteobacterial endosymbiont. The endosymbiont genome displays features consistent with ongoing genome reduction such as large proportions of pseudogenes and insertion elements. The genome encodes functions commonly found in deep-sea vent chemoautotrophs such as sulfur oxidation and carbon fixation. Stable carbon isotope ((13)C)-labeling experiments confirmed the endosymbiont chemoautotrophy. The genome also includes an intact hydrogenase gene cluster that potentially has been horizontally transferred from phylogenetically distant bacteria. Notable findings include the presence and transcription of genes for flagellar assembly, through which proteins are potentially exported from bacterium to the host. Symbionts of snail individuals exhibited extreme genetic homogeneity, showing only two synonymous changes in 19 different genes (13 810 positions in total) determined for 32 individual gastropods collected from a single colony at one time. The extremely low genetic individuality in endosymbionts probably reflects that the stringent symbiont selection by host prevents the random genetic drift in the small population of horizontally transmitted symbiont. This study is the first complete genome analysis of gastropod endosymbiont and offers an opportunity to study genome evolution in a recently evolved endosymbiont.

The Scientific Legacy of the CARIACO Ocean Time-Series Program.

PubMed

Muller-Karger, Frank E; Astor, Yrene M; Benitez-Nelson, Claudia R; Buck, Kristen N; Fanning, Kent A; Lorenzoni, Laura; Montes, Enrique; Rueda-Roa, Digna T; Scranton, Mary I; Tappa, Eric; Taylor, Gordon T; Thunell, Robert C; Troccoli, Luis; Varela, Ramon

2018-06-11

TheCARIACO(Carbon Retention in a Colored Ocean) Ocean Time-Series Program station, located at 10.50°N, 64.66°W, observed biogeochemical and ecological processes in the Cariaco Basin of the southwestern Caribbean Sea from November 1995 to January 2017. The program completed 232 monthly core cruises, 40 sediment trap deployment cruises, and 40 microbiogeochemical process cruises. Upwelling along the southern Caribbean Sea occurs from approximately November to August. High biological productivity (320-628 g C m -2 y -1 ) leads to large vertical fluxes of particulate organic matter, but only approximately 9-10 g C m -2 y -1 fall to the bottom sediments (∼1-3% of primary production). A diverse community of heterotrophic and chemoautotrophic microorganisms, viruses, and protozoa thrives within the oxic-anoxic interface. A decrease in upwelling intensity from approximately 2003 to 2013 and the simultaneous overfishing of sardines in the region led to diminished phytoplankton bloom intensities, increased phytoplankton diversity, and increased zooplankton densities. The deepest waters of the Cariaco Basin exhibited long-term positive trends in temperature, salinity, hydrogen sulfide, ammonia, phosphate, methane, and silica. Earthquakes and coastal flooding also resulted in the delivery of sediment to the seafloor. The program's legacy includes climate-quality data from suboxic and anoxic habitats and lasting relationships between international researchers. Expected final online publication date for the Annual Review of Marine Science Volume 11 is January 3, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

An extensive reef system at the Amazon River mouth.

PubMed

Moura, Rodrigo L; Amado-Filho, Gilberto M; Moraes, Fernando C; Brasileiro, Poliana S; Salomon, Paulo S; Mahiques, Michel M; Bastos, Alex C; Almeida, Marcelo G; Silva, Jomar M; Araujo, Beatriz F; Brito, Frederico P; Rangel, Thiago P; Oliveira, Braulio C V; Bahia, Ricardo G; Paranhos, Rodolfo P; Dias, Rodolfo J S; Siegle, Eduardo; Figueiredo, Alberto G; Pereira, Renato C; Leal, Camille V; Hajdu, Eduardo; Asp, Nils E; Gregoracci, Gustavo B; Neumann-Leitão, Sigrid; Yager, Patricia L; Francini-Filho, Ronaldo B; Fróes, Adriana; Campeão, Mariana; Silva, Bruno S; Moreira, Ana P B; Oliveira, Louisi; Soares, Ana C; Araujo, Lais; Oliveira, Nara L; Teixeira, João B; Valle, Rogerio A B; Thompson, Cristiane C; Rezende, Carlos E; Thompson, Fabiano L

2016-04-01

Large rivers create major gaps in reef distribution along tropical shelves. The Amazon River represents 20% of the global riverine discharge to the ocean, generating up to a 1.3 × 10(6)-km(2) plume, and extensive muddy bottoms in the equatorial margin of South America. As a result, a wide area of the tropical North Atlantic is heavily affected in terms of salinity, pH, light penetration, and sedimentation. Such unfavorable conditions were thought to imprint a major gap in Western Atlantic reefs. We present an extensive carbonate system off the Amazon mouth, underneath the river plume. Significant carbonate sedimentation occurred during lowstand sea level, and still occurs in the outer shelf, resulting in complex hard-bottom topography. A permanent near-bottom wedge of ocean water, together with the seasonal nature of the plume's eastward retroflection, conditions the existence of this extensive (~9500 km(2)) hard-bottom mosaic. The Amazon reefs transition from accretive to erosional structures and encompass extensive rhodolith beds. Carbonate structures function as a connectivity corridor for wide depth-ranging reef-associated species, being heavily colonized by large sponges and other structure-forming filter feeders that dwell under low light and high levels of particulates. The oxycline between the plume and subplume is associated with chemoautotrophic and anaerobic microbial metabolisms. The system described here provides several insights about the responses of tropical reefs to suboptimal and marginal reef-building conditions, which are accelerating worldwide due to global changes.

Life in the dark: metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism.

PubMed

Tetu, Sasha G; Breakwell, Katy; Elbourne, Liam D H; Holmes, Andrew J; Gillings, Michael R; Paulsen, Ian T

2013-06-01

Beneath Australia's large, dry Nullarbor Plain lies an extensive underwater cave system, where dense microbial communities known as 'slime curtains' are found. These communities exist in isolation from photosynthetically derived carbon and are presumed to be chemoautotrophic. Earlier work found high levels of nitrite and nitrate in the cave waters and a high relative abundance of Nitrospirae in bacterial 16S rRNA clone libraries. This suggested that these communities may be supported by nitrite oxidation, however, details of the inorganic nitrogen cycling in these communities remained unclear. Here we report analysis of 16S rRNA amplicon and metagenomic sequence data from the Weebubbie cave slime curtain community. The microbial community is comprised of a diverse assortment of bacterial and archaeal genera, including an abundant population of Thaumarchaeota. Sufficient thaumarchaeotal sequence was recovered to enable a partial genome sequence to be assembled, which showed considerable synteny with the corresponding regions in the genome of the autotrophic ammonia oxidiser Nitrosopumilus maritimus SCM1. This partial genome sequence, contained regions with high sequence identity to the ammonia mono-oxygenase operon and carbon fixing 3-hydroxypropionate/4-hydroxybutyrate cycle genes of N. maritimus SCM1. Additionally, the community, as a whole, included genes encoding key enzymes for inorganic nitrogen transformations, including nitrification and denitrification. We propose that the Weebubbie slime curtain community represents a distinctive microbial ecosystem, in which primary productivity is due to the combined activity of archaeal ammonia-oxidisers and bacterial nitrite oxidisers.

Serine 363 of a hydrophobic region of Archaeal ribulose 1,5-bisphosphate carboxylase/oxygenase from Archaeoglobus fulgidus and Thermococcus kodakaraensis affects CO 2/O 2 substrate specificity and oxygen sensitivity

DOE PAGES

Kreel, Nathan E.; Tabita, F. Robert; Berg, Ivan

2015-09-18

Archaeal ribulose 1, 5-bisphospate carboxylase/oxygenase (RubisCO) is differentiated from other RubisCO enzymes and is classified as a form III enzyme, as opposed to the form I and form II RubisCOs typical of chemoautotrophic bacteria and prokaryotic and eukaryotic phototrophs. The form III enzyme from archaea is particularly interesting as several of these proteins exhibit unusual and reversible sensitivity to molecular oxygen, including the enzyme from Archaeoglobus fulgidus. Previous studies with A. fulgidus RbcL2 had shown the importance of Met-295 in oxygen sensitivity and pointed towards the potential significance of another residue (Ser-363) found in a hydrophobic pocket that is conservedmore » in all RubisCO proteins. In the current study, further structure/function studies have been performed focusing on Ser-363 of A. fulgidus RbcL2; various changes in this and other residues of the hydrophobic pocket point to and definitively establish the importance of Ser-363 with respect to interactions with oxygen. In addition, previous findings had indicated discrepant CO 2/O 2 specificity determinations of the Thermococcus kodakaraensis RubisCO, a close homolog of A. fulgidus RbcL2. As a result, it is shown here that the T. kodakaraensis enzyme exhibits a similar substrate specificity as the A. fulgidus enzyme and is also oxygen sensitive, with equivalent residues involved in oxygen interactions.« less

Temporal change in megafauna at the Rose Garden hydrothermal vent (Galapagos Rift; eastern tropical Pacific)

NASA Astrophysics Data System (ADS)

Hessler, Robert R.; Smithey, William M.; Boudrias, Michel A.; Keller, Clifford H.; Lutz, Richard A.; Childress, James J.

1988-10-01

Hydrothermal vent communities must undergo substantial temporal change because of their dynamic physical milieu. This was verified in March 1985, when the Rose Garden hydrothermal vent on the Galapagos Rift was revisited after 5 1/4 years' absence. Comparison of photographs from the two visits revealed considerable faunal change. Among the hosts to chemoautotrophic bacteria, vestimentiferans were reduced from dominance to very low numbers. The mytilid was now extremely abundant and dominated vent openings. Vesicomyids also were more abundant. In general, vent-field suspension feeders had declined; anemones were distinctly less abundant, and siphonophores and enteropneusts were virtually absent. The decline of serpulids was likely, but less obvious. Of the mobile scavengers and carnivores, both galatheids and whelks were distincly more common. These community changes appear to result from both continuing recruitment and changes in the physical milieu. While the growth of some populations could have resulted from expanding opportunities, the population of at least one, the vesicomyid, had not achieved carrying capacity in 1979, and this could have pertained to others as well. The decrease of vestimentiferans may have been caused by declining vent-water flux, a process that would favor mytilids, or more complete vent-water filtration by the mytilids themselves. The same factors also could explain the reduction of vent-field filter feeders. These observations suggest that early stages in the cycle of Galapagos-type vent communities are likely to be dominated by vestimentiferans, but that bivalves will replace them with time.

Heterotrophic and Autotrophic Microbial Populations in Cold Perennial Springs of the High Arctic ▿ †

PubMed Central

Perreault, Nancy N.; Greer, Charles W.; Andersen, Dale T.; Tille, Stefanie; Lacrampe-Couloume, Georges; Lollar, Barbara Sherwood; Whyte, Lyle G.

2008-01-01

The saline springs of Gypsum Hill in the Canadian high Arctic are a rare example of cold springs originating from deep groundwater and rising to the surface through thick permafrost. The heterotrophic bacteria and autotrophic sulfur-oxidizing bacteria (up to 40% of the total microbial community) isolated from the spring waters and sediments were classified into four phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) based on 16S rRNA gene analysis; heterotrophic isolates were primarily psychrotolerant, salt-tolerant, facultative anaerobes. Some of the isolates contained genes for thiosulfate oxidation (soxB) and anoxygenic photosynthesis (pufM), possibly enabling the strains to better compete in these sulfur-rich environments subject to long periods of illumination in the Arctic summer. Although leucine uptake by the spring water microbial community was low, CO2 uptake was relatively high under dark incubation, reinforcing the idea that primary production by chemoautotrophs is an important process in the springs. The small amounts of hydrocarbons in gases exsolving from the springs (0.38 to 0.51% CH4) were compositionally and isotopically consistent with microbial methanogenesis and possible methanotrophy. Anaerobic heterotrophic sulfur oxidation and aerobic autotrophic sulfur oxidation activities were demonstrated in sediment slurries. Overall, our results describe an active microbial community capable of sustainability in an extreme environment that experiences prolonged periods of continuous light or darkness, low temperatures, and moderate salinity, where life seems to rely on chemolithoautotrophy. PMID:18805995

High bicarbonate assimilation in the dark by Arctic bacteria.

PubMed

Alonso-Sáez, Laura; Galand, Pierre E; Casamayor, Emilio O; Pedrós-Alió, Carlos; Bertilsson, Stefan

2010-12-01

Although both autotrophic and heterotrophic microorganisms incorporate CO₂ in the dark through different metabolic pathways, this process has usually been disregarded in oxic marine environments. We studied the significance and mediators of dark bicarbonate assimilation in dilution cultures inoculated with winter Arctic seawater. At stationary phase, bicarbonate incorporation rates were high (0.5-2.5 μg C L⁻¹ d⁻¹) and correlated with rates of bacterial heterotrophic production, suggesting that most of the incorporation was due to heterotrophs. Accordingly, very few typically chemoautotrophic bacteria were detected by 16S rRNA gene cloning. The genetic analysis of the biotin carboxylase gene accC putatively involved in archaeal CO₂ fixation did not yield any archaeal sequence, but amplified a variety of bacterial carboxylases involved in fatty acids biosynthesis, anaplerotic pathways and leucine catabolism. Gammaproteobacteria dominated the seawater cultures (40-70% of cell counts), followed by Betaproteobacteria and Flavobacteria as shown by catalyzed reporter deposition fluorescence in situ hybridization (CARDFISH). Both Beta- and Gammaproteobacteria were active in leucine and bicarbonate uptake, while Flavobacteria did not take up bicarbonate, as measured by microautoradiography combined with CARDFISH. Within Gammaproteobacteria, Pseudoalteromonas-Colwellia and Oleispira were very active in bicarbonate uptake (ca. 30 and 70% of active cells, respectively), while the group Arctic96B-16 did not take up bicarbonate. Our results suggest that, potentially, the incorporation of CO₂ can be relevant for the metabolism of specific Arctic heterotrophic phylotypes, promoting the maintenance of their cell activity and/or longer survival under resource depleted conditions.

Ferredoxin:thioredoxin reductase (FTR) links the regulation of oxygenic photosynthesis to deeply rooted bacteria.

PubMed

Balsera, Monica; Uberegui, Estefania; Susanti, Dwi; Schmitz, Ruth A; Mukhopadhyay, Biswarup; Schürmann, Peter; Buchanan, Bob B

2013-02-01

Uncovered in studies on photosynthesis 35 years ago, redox regulation has been extended to all types of living cells. We understand a great deal about the occurrence, function, and mechanism of action of this mode of regulation, but we know little about its origin and its evolution. To help fill this gap, we have taken advantage of available genome sequences that make it possible to trace the phylogenetic roots of members of the system that was originally described for chloroplasts-ferredoxin, ferredoxin:thioredoxin reductase (FTR), and thioredoxin as well as target enzymes. The results suggest that: (1) the catalytic subunit, FTRc, originated in deeply rooted microaerophilic, chemoautotrophic bacteria where it appears to function in regulating CO(2) fixation by the reverse citric acid cycle; (2) FTRc was incorporated into oxygenic photosynthetic organisms without significant structural change except for addition of a variable subunit (FTRv) seemingly to protect the Fe-S cluster against oxygen; (3) new Trxs and target enzymes were systematically added as evolution proceeded from bacteria through the different types of oxygenic photosynthetic organisms; (4) an oxygenic type of regulation preceded classical light-dark regulation in the regulation of enzymes of CO(2) fixation by the Calvin-Benson cycle; (5) FTR is not universally present in oxygenic photosynthetic organisms, and in certain early representatives is seemingly functionally replaced by NADP-thioredoxin reductase; and (6) FTRc underwent structural diversification to meet the ecological needs of a variety of bacteria and archaea.

When did decapods invade hydrothermal vents? Clues from the Western Pacific and Indian Oceans.

PubMed

Yang, Jin-Shu; Lu, Bo; Chen, Dian-Fu; Yu, Yan-Qin; Yang, Fan; Nagasawa, Hiromichi; Tsuchida, Shinji; Fujiwara, Yoshihiro; Yang, Wei-Jun

2013-02-01

Hydrothermal vents are typically located in midocean ridges and back-arc basins and are usually generated by the movement of tectonic plates. Life thrives in these environments despite the extreme conditions. In addition to chemoautotrophic bacteria, decapod crustaceans are dominant in many of the hydrothermal vents discovered to date. Contrary to the hypothesis that these species are remnants of relic fauna, increasing evidence supports the notion that hydrothermal vent decapods have diversified in more recent times with previous research attributing the origin of alvinocarid shrimps to the Miocene. This study investigated seven representative decapod species from four hydrothermal vents throughout the Western Pacific and Indian Oceans. A partitioned mix-model phylogenomic analysis of mitochondrial DNA produced a consistent phylogenetic topology of these vent-endemic species. Additionally, molecular dating analysis calibrated using multiple fossils suggested that both bythograeid crabs and alvinocarid shrimps originated in the late Mesozoic and early Cenozoic. Although of limited sampling, our estimates support the extinction/repopulation hypothesis, which postulates recent diversification times for most hydrothermal vent species due to their mass extinction by global deep-water anoxic/dysoxic events during the Late Cretaceous and Early Tertiary. The continental-derived property of the West Pacific province is compatible with the possibility that vent decapods diversified from ancestors from shallow-water regions such as cold seeps. Our results move us a step closer toward understanding the evolutionary origin of hydrothermal vent species and their distribution in the Western Pacific-Indian Ocean Region.

Spatial elements of mortality risk in old-growth forests

USGS Publications Warehouse

Das, Adrian; Battles, John; van Mantgem, Phillip J.; Stephenson, Nathan L.

2008-01-01

For many species of long-lived organisms, such as trees, survival appears to be the most critical vital rate affecting population persistence. However, methods commonly used to quantify tree death, such as relating tree mortality risk solely to diameter growth, almost certainly do not account for important spatial processes. Our goal in this study was to detect and, if present, to quantify the relevance of such processes. For this purpose, we examined purely spatial aspects of mortality for four species, Abies concolor, Abies magnifica, Calocedrus decurrens, and Pinus lambertiana, in an old-growth conifer forest in the Sierra Nevada of California, USA. The analysis was performed using data from nine fully mapped long-term monitoring plots.In three cases, the results unequivocally supported the inclusion of spatial information in models used to predict mortality. For Abies concolor, our results suggested that growth rate may not always adequately capture increased mortality risk due to competition. We also found evidence of a facilitative effect for this species, with mortality risk decreasing with proximity to conspecific neighbors. For Pinus lambertiana, mortality risk increased with density of conspecific neighbors, in keeping with a mechanism of increased pathogen or insect pressure (i.e., a Janzen-Connell type effect). Finally, we found that models estimating risk of being crushed were strongly improved by the inclusion of a simple index of spatial proximity.Not only did spatial indices improve models, those improvements were relevant for mortality prediction. For P. lambertiana, spatial factors were important for estimation of mortality risk regardless of growth rate. For A. concolor, although most of the population fell within spatial conditions in which mortality risk was well described by growth, trees that died occurred outside those conditions in a disproportionate fashion. Furthermore, as stands of A. concolor become increasingly dense, such spatial factors are likely to become increasingly important. In general, models that fail to account for spatial pattern are at risk of failure as conditions change.

Atmospheric deposition and solute export in giant sequoia: mixed conifer watersheds in the Sierra Nevada, California

USGS Publications Warehouse

Stohlgren, Thomas J.; Melack, John M.; Esperanza, Anne M.; Parsons, David J.

1991-01-01

Atmospheric depostion and stream discharge and solutes were measured for three years (September 1984 - August 1987) in two mixed conifer watersheds in Sequoia National Park, in the southern Sierra Nevada of California. The Log Creek watershed (50 ha, 2067-2397 m elev.) is drained by a perennial stream, while Tharp's Creek watershed (13 ha, 2067-2255 m elev.) contains an intermittent stream. Dominant trees in the area include Abies concolor (white fir), Sequoiadendron giganteum (giant sequoia), A. magnifica (red fir), and Pinus lambertiana (sugar pine). Bedrock is predominantly granite and granodiorite, and the soils are mostly Pachic Xerumbrepts. Over the three year period, sulfate (SO42-), nitrate (NO3-), and chloride (Cl-) were the major anions in bulk precipitation with volume-weighted average concentrations of 12.6, 12.3 and 10.0 μeq/1, respectively. Annual inputs of NO3-N, NH4-N and SO4-S from wet deposition were about 60 to 75% of those reported from bulk deposition collectors. Discharge from the two watersheds occurs primarily during spring snowmelt. Solute exports from Log and Tharp's Creeks were dominated by HCO3-, Ca2+ and Na+, while H+, NO3-, NH4+ and PO43- outputs were relatively small. Solute concentrations were weakly correlated with instantaneous stream flow for all solutes (r2 3- (Log Cr. r2=0.72; Tharp's Cr. r2=0.38), Na+ (Log Cr. r2=0.56; Tharp's Cr. r2=0.47), and silicate (Log Cr. r2=0.71; Tharp's Cr. r2=0.49). Mean annual atmospheric contributions of NO3-N (1.6 kg ha-1), NH4-N (1.7 kg ha-1), and SO4-S (1.8 kg ha-1), which are associated with acidic deposition, greatly exceed hydrologic losses. Annual watershed yields (expressed as eq ha-1) of HCO3- exceeded by factors of 2.5 to 37 the annual atmospheric deposition of H+.

Inorganic carbon fixation by chemosynthetic ectosymbionts and nutritional transfers to the hydrothermal vent host-shrimp Rimicaris exoculata

PubMed Central

Ponsard, Julie; Cambon-Bonavita, Marie-Anne; Zbinden, Magali; Lepoint, Gilles; Joassin, André; Corbari, Laure; Shillito, Bruce; Durand, Lucile; Cueff-Gauchard, Valérie; Compère, Philippe

2013-01-01

The shrimp Rimicaris exoculata dominates several hydrothermal vent ecosystems of the Mid-Atlantic Ridge and is thought to be a primary consumer harbouring a chemoautotrophic bacterial community in its gill chamber. The aim of the present study was to test current hypotheses concerning the epibiont's chemoautotrophy, and the mutualistic character of this association. In-vivo experiments were carried out in a pressurised aquarium with isotope-labelled inorganic carbon (NaH13CO3 and NaH14CO3) in the presence of two different electron donors (Na2S2O3 and Fe2+) and with radiolabelled organic compounds (14C-acetate and 3H-lysine) chosen as potential bacterial substrates and/or metabolic by-products in experiments mimicking transfer of small biomolecules from epibionts to host. The bacterial epibionts were found to assimilate inorganic carbon by chemoautotrophy, but many of them (thick filaments of epsilonproteobacteria) appeared versatile and able to switch between electron donors, including organic compounds (heterotrophic acetate and lysine uptake). At least some of them (thin filamentous gammaproteobacteria) also seem capable of internal energy storage that could supply chemosynthetic metabolism for hours under conditions of electron donor deprivation. As direct nutritional transfer from bacteria to host was detected, the association appears as true mutualism. Import of soluble bacterial products occurs by permeation across the gill chamber integument, rather than via the digestive tract. This first demonstration of such capabilities in a decapod crustacean supports the previously discarded hypothesis of transtegumental absorption of dissolved organic matter or carbon as a common nutritional pathway. PMID:22914596

Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil▿†

PubMed Central

Jung, Man-Young; Park, Soo-Je; Min, Deullae; Kim, Jin-Seog; Rijpstra, W. Irene C.; Sinninghe Damsté, Jaap S.; Kim, Geun-Joong; Madsen, Eugene L.; Rhee, Sung-Keun

2011-01-01

Soil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizing Archaea from soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain MY1) in a highly enriched culture derived from agricultural soil. Fluorescence in situ hybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cells. Clone libraries of both 16S rRNA and archaeal amoA genes featured a single sequence each. No bacterial amoA genes could be detected by PCR. A [13C]bicarbonate assimilation assay showed stoichiometric incorporation of 13C into Archaea-specific glycerol dialkyl glycerol tetraethers. Strain MY1 falls phylogenetically within crenarchaeal group I.1a; sequence comparisons to “Candidatus Nitrosopumilus maritimus” revealed 96.9% 16S rRNA and 89.2% amoA gene similarities. Completed growth assays showed strain MY1 to be chemoautotrophic, mesophilic (optimum at 25°C), neutrophilic (optimum at pH 6.5 to 7.0), and nonhalophilic (optimum at 0.2 to 0.4% salinity). Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB). The yield of the greenhouse gas N2O in the strain MY1 culture was lower but comparable to that of soil AOB. We propose that this new soil ammonia-oxidizing archaeon be designated “Candidatus Nitrosoarchaeum koreensis.” PMID:22003023

Microbial and biogeochernical processes Soda Lake, Nevada

USGS Publications Warehouse

Oremland, R.S.; Cloern, J.E.; Sofer, Z.; Smith, R.L.; Culbertson, C.W.; Zehr, J.; Miller, L.; Cole, B.; Harvey, R.; Iversen, N.; Klug, M.; Des Marais, D J; Rau, G.

1988-01-01

Meromictic, alkaline lakes represent modern-day analogues of lacustrine source rock depositional environments. In order to further our understanding of how these lakes function in terms of limnological and biogeochemical processes, we have conducted an interdisciplinary study of Big Soda Lake. Annual mixolimnion productivity (ca. 500 g m-2) is dominated by a winter diatom bloom (60% of annual) caused by upward transport of ammonia to the epilimnion. The remainder of productivity is attributable to chemoautotrophs (30%) and photosynthetic bacteria (10%) present at the oxic -anoxic interface from May to November. Studies of bacterial heterotrophy and particulate fluxes in the water column indicate that about 90% of annual productivity is remineralized in the mixolimnion, primarily by fermentative bacteria. However, high rates of sulphate reduction (9-29 mmol m-2 yr-1) occur in the monimolimnion waters, which could remineralize most (if not all) of the primary productivity. This discrepancy has not as yet been fully explained. Low rates of methanogenesis also occur in the monimolimnion waters and sediments. Most of the methane is consumed by anaerobic methane oxidation occurring in the monimolimnion water column. Other bacterial processes occurring in the lake are also discussed. Preliminary studies have been made on the organic geochemistry of the monimolimnion sediments. Carbon-14-dating indicates a lower depositional rate prior to meromixis and a downcore enrichment in 13C of organic carbon and chlorophyll derivatives. Hydrous pyrolysis experiments indicate that the sediment organic matter is almost entirely derived from the water column with little or no contribution from terrestrial sources. The significance of the organics released by hydrous pyrolysis is discussed.

The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis.

PubMed

Dmytrenko, Oleg; Russell, Shelbi L; Loo, Wesley T; Fontanez, Kristina M; Liao, Li; Roeselers, Guus; Sharma, Raghav; Stewart, Frank J; Newton, Irene L G; Woyke, Tanja; Wu, Dongying; Lang, Jenna Morgan; Eisen, Jonathan A; Cavanaugh, Colleen M

2014-10-23

Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the ability to maintain it under laboratory conditions. To better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. The physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle.

Dissimilatory arsenate reduction with sulfide as the electron donor--Experiments with Mono Lake water and isolation of strain MLMS-1, a chemoautotrophic arsenate-respirer

USGS Publications Warehouse

Hoeft, Shelley E.; Kulp, Thomas R.; Stolz, John F.; Hollibaugh, James T.; Oremland, Ronald S.

2004-01-01

Anoxic bottom water from Mono Lake, California, can biologically reduce added arsenate without any addition of electron donors. Of the possible in situ inorganic electron donors present, only sulfide was sufficiently abundant to drive this reaction. We tested the ability of sulfide to serve as an electron donor for arsenate reduction in experiments with lake water. Reduction of arsenate to arsenite occurred simultaneously with the removal of sulfide. No loss of sulfide occurred in controls without arsenate or in sterilized samples containing both arsenate and sulfide. The rate of arsenate reduction in lake water was dependent on the amount of available arsenate. We enriched for a bacterium that could achieve growth with sulfide and arsenate in a defined, mineral medium and purified it by serial dilution. The isolate, strain MLMS-1, is a gram-negative, motile curved rod that grows by oxidizing sulfide to sulfate while reducing arsenate to arsenite. Chemoautotrophy was confirmed by the incorporation of H14CO3− into dark-incubated cells, but preliminary gene probing tests with primers for ribulose-1,5-biphosphate carboxylase/oxygenase did not yield PCR-amplified products. Alignment of 16S rRNA sequences indicated that strain MLMS-1 was in the δ-Proteobacteria, located near sulfate reducers like Desulfobulbus sp. (88 to 90% similarity) but more closely related (97%) to unidentified sequences amplified previously from Mono Lake. However, strain MLMS-1 does not grow with sulfate as its electron acceptor.

Acquisition of epibiotic bacteria along the life cycle of the hydrothermal shrimp Rimicaris exoculata.

PubMed

Guri, Mathieu; Durand, Lucile; Cueff-Gauchard, Valérie; Zbinden, Magali; Crassous, Philippe; Shillito, Bruce; Cambon-Bonavita, Marie-Anne

2012-03-01

The caridean shrimp Rimicaris exoculata dominates the fauna at several Mid-Atlantic Ridge hydrothermal vent sites. This shrimp has an enlarged gill chamber, harboring a dense ectosymbiotic community of chemoautotrophic bacteria associated with mineral oxide deposits. Until now, their acquisition is not fully understood. At three hydrothermal vent sites, we analyzed the epibionts diversity at different moult stages and also in the first stages of the shrimp life (eggs, hatched eggs (with larvae) and juveniles). Hatched eggs associated with young larvae were collected for the first time directly from gravid females at the Logachev vent site during the Serpentine cruise. An approach using 16S rRNA clone libraries, scanning and transmission electron microscopy, and fluorescent in situ hybridization was used. Molecular results and microscope observations indicated a switch in the composition of the bacterial community between early R. exoculata life cycle stage (egg libraries dominated by the Gammaproteobacteria) and later stages (juvenile/adult libraries dominated by the Epsilonproteobacteria). We hypothesized that the epibiotic phylotype composition could vary according to the life stage of the shrimp. Our results confirmed the occurrence of a symbiosis with Gammaproteobacteria and Epsilonproteobacteria, but more complex than previously assumed. We revealed the presence of active type-I methanotrophic bacteria colonizing the cephalothorax of shrimps from the Rainbow site. They were also present on the eggs from the Logachev site. This could be the first 'epibiotic' association between methanotrophic bacteria and hydrothermal vent crustacean. We discuss possible transmission pathways for epibionts linked to the shrimp life cycle.

Acquisition of epibiotic bacteria along the life cycle of the hydrothermal shrimp Rimicaris exoculata

PubMed Central

Guri, Mathieu; Durand, Lucile; Cueff-Gauchard, Valérie; Zbinden, Magali; Crassous, Philippe; Shillito, Bruce; Cambon-Bonavita, Marie-Anne

2012-01-01

The caridean shrimp Rimicaris exoculata dominates the fauna at several Mid-Atlantic Ridge hydrothermal vent sites. This shrimp has an enlarged gill chamber, harboring a dense ectosymbiotic community of chemoautotrophic bacteria associated with mineral oxide deposits. Until now, their acquisition is not fully understood. At three hydrothermal vent sites, we analyzed the epibionts diversity at different moult stages and also in the first stages of the shrimp life (eggs, hatched eggs (with larvae) and juveniles). Hatched eggs associated with young larvae were collected for the first time directly from gravid females at the Logachev vent site during the Serpentine cruise. An approach using 16S rRNA clone libraries, scanning and transmission electron microscopy, and fluorescent in situ hybridization was used. Molecular results and microscope observations indicated a switch in the composition of the bacterial community between early R. exoculata life cycle stage (egg libraries dominated by the Gammaproteobacteria) and later stages (juvenile/adult libraries dominated by the Epsilonproteobacteria). We hypothesized that the epibiotic phylotype composition could vary according to the life stage of the shrimp. Our results confirmed the occurrence of a symbiosis with Gammaproteobacteria and Epsilonproteobacteria, but more complex than previously assumed. We revealed the presence of active type-I methanotrophic bacteria colonizing the cephalothorax of shrimps from the Rainbow site. They were also present on the eggs from the Logachev site. This could be the first ‘epibiotic' association between methanotrophic bacteria and hydrothermal vent crustacean. We discuss possible transmission pathways for epibionts linked to the shrimp life cycle. PMID:21993397

Ecogenomic characterization of a marine microorganism belonging to a Firmicutes lineage that is widespread in both terrestrial and oceanic subsurface environments

NASA Astrophysics Data System (ADS)

Jungbluth, S.; Glavina del Rio, T.; Tringe, S. G.; Stepanauskas, R.; Rappe, M. S.

2015-12-01

Large-volumes of basalt-hosted fluids from the sediment-covered subseafloor were collected in July 2011 from a horizon extending 29-117 meters below the sediment-rock interface at borehole 1362B, as well as from a deep horizon extending 193-292 meters below the sediment-rock interface at borehole 1362A, which are two of the latest generation of borehole observatories on the Juan de Fuca Ridge flank in the Northeast Pacific Ocean. Environmental DNA was sequenced from one fluid sample collected from each borehole, and a genomic bin related to the terrestrial Candidatus Desulforudis audaxviator lineage within the Firmicutes phylum of bacteria was identified. The near-complete bacterial genome, herein named Candidatus Desulfopertinax inferamarinus, is composed of six scaffolds totaling 1.78 Mbp in length. Despite vast differences in geography and environment of origin, phylogenomic analysis indicate that D. inferamarinus and D. audaxviator form a monophyletic clade to the exclusion of all other sequenced genomes. Similar to its terrestrial relative, the draft genome of the marine D. inferamarinus revealed a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that is capable of synthesizing all amino acids and fixing inorganic carbon via the Wood-Ljungdahl pathway. Unlike the terrestrial clade, relatively few integrases and transposases were identified. The marine genome described here provides evidence that a life-style adapted to the isolated deep subsurface environment is a general feature of the broader, globally-distributed Desulforudis/Desulfopertinax lineage and provides insight into the adaptations required for microbial life in the marine versus terrestrial deep biospheres.

Characterization of a Planctomycetal Organelle: a Novel Bacterial Microcompartment for the Aerobic Degradation of Plant Saccharides

PubMed Central

Erbilgin, Onur; McDonald, Kent L.

2014-01-01

Bacterial microcompartments (BMCs) are organelles that encapsulate functionally linked enzymes within a proteinaceous shell. The prototypical example is the carboxysome, which functions in carbon fixation in cyanobacteria and some chemoautotrophs. It is increasingly apparent that diverse heterotrophic bacteria contain BMCs that are involved in catabolic reactions, and many of the BMCs are predicted to have novel functions. However, most of these putative organelles have not been experimentally characterized. In this study, we sought to discover the function of a conserved BMC gene cluster encoded in the majority of the sequenced planctomycete genomes. This BMC is especially notable for its relatively simple genetic composition, its remote phylogenetic position relative to characterized BMCs, and its apparent exclusivity to the enigmatic Verrucomicrobia and Planctomycetes. Members of the phylum Planctomycetes are known for their morphological dissimilarity to the rest of the bacterial domain: internal membranes, reproduction by budding, and lack of peptidoglycan. As a result, they are ripe for many discoveries, but currently the tools for genetic studies are very limited. We expanded the genetic toolbox for the planctomycetes and generated directed gene knockouts of BMC-related genes in Planctomyces limnophilus. A metabolic activity screen revealed that BMC gene products are involved in the degradation of a number of plant and algal cell wall sugars. Among these sugars, we confirmed that BMCs are formed and required for growth on l-fucose and l-rhamnose. Our results shed light on the functional diversity of BMCs as well as their ecological role in the planctomycetes, which are commonly associated with algae. PMID:24487526

Chemosynthetic microbial activity at Mid-Atlantic Ridge hydrothermal vent sites

NASA Astrophysics Data System (ADS)

Wirsen, Carl O.; Jannasch, Holger W.; Molyneaux, Stephen J.

1993-06-01

Chemosynthetic production of microbial biomass, determined by 14CO2 fixation and enzymatic (RuBisCo) activity, at the Mid-Atlantic Ridge (MAR) 23° and 26°N vent sites was found in various niches: warm water emissions, loosely rock-attached flocculent material, dense morphologically diverse bacterial mats covering the surfaces of polymetal sulfide deposits, and filamentous microbes on the carapaces of shrimp (Rimicaris exoculata). The bacterial mats on polymetal sulfide surfaces contained unicellular and filamentous bacteria which appeared to use as their chemolithotrophic electron or energy source either dissolved reduced minerals from vent emissions, mainly sulfur compounds, or solid metal sulfide deposits, mainly pyrite. Moderately thermophilic Chemosynthetic activity was observed in carbon dioxide fixation experiments and in enrichments, but no thermophilic aerobic sulfur oxidizers could be isolated. Both obligate and facultative chemoautotrophs growing at mesophilic temperatures were isolated from all chemosynthetically active surface scrapings. The obligate autotrophs could oxidize sterilized MAR natural sulfide deposits as well as technical pyrite at near neutral pH, in addition to dissolved reduced sulfur compounds. While the grazing by shrimp on the surface mats of MAR metal sulfide deposits was observed and deemed important, the animals' primary occurrence in dense swarms near vent emissions suggests that they were feeding at these sites, where conditions for Chemosynthetic growth of their filamentous microbial epiflora were optimal. The data show that the transformation of geothermal energy at the massive polymetal sulfide deposits of the MAR is based on the lithoautotrophic oxidation of soluble sulfides and pyrites into microbial biomass.

The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dmytrenko, Oleg; Russell, Shelbi L.; Loo, Wesley T.

Background: Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and themore » ability to maintain it under laboratory conditions. To better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. Results: Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.86 Mb), GC-rich (50.4percent), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. Conclusions: The physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle« less

The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dmytrenko, Oleg; Russell, Shelbi L.; Loo, Wesley T.

Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the abilitymore » to maintain it under laboratory conditions. Here, to better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. In conclusion, the physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle.« less

Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps

PubMed Central

Zhang, Xian; Liu, Xueduan; Liang, Yili; Xiao, Yunhua; Ma, Liyuan; Guo, Xue; Miao, Bo; Liu, Hongwei; Peng, Deliang; Huang, Wenkun; Yin, Huaqun

2017-01-01

The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist. PMID:28529505

Strong pathways for incorporation of terrestrially derived organic matter into benthic communities

NASA Astrophysics Data System (ADS)

McLeod, Rebecca J.; Wing, Stephen R.

2009-05-01

In Fiordland, New Zealand, large volumes of organic matter are deposited into the marine environment from pristine forested catchments. Analyses of δ15N, δ13C and δ34S were employed to determine whether these inputs were contributing to marine food webs via assimilation by common macroinvertebrates inhabiting the inner reaches of the fjords. Terrestrially derived organic matter (TOM) had values of δ15N, δ13C and δ34S that were distinct from other carbon source pools, providing sufficient power to quantify the contribution of TOM to the benthic food web. Isotopic values among macroinvertebrates varied significantly, with consistently low values of δ15N, δ13C and δ34S for the abundant deposit feeders Echinocardium cordatum (Echinodermata) and Pectinaria australis (Annelida), indicating assimilation of TOM. High concentrations of bacterial fatty acid biomarkers in E. cordatum, and values of δ13C of these biomarkers similar to TOM (-27 to -30‰) confirmed that TOM is indirectly assimilated by these sea urchins via heterotrophic bacteria. TOM was also found to enter the infaunal food web via chemoautotrophic bacteria that live symbiotically within Solemya parkinsonii (Bivalvia). Echinocardium cordatum, Pectinaria australis and S. parkinsonii comprised up to 33.5% of the biomass of the macroinfaunal community, and thus represent strong pathways for movement of organic matter from the forested catchments into the benthic food web. This demonstration of connectivity among adjacent marine and terrestrial habitats has important implications for coastal land management, and highlights the importance of intact coastal forests to marine ecosystem function.

Physical Conditions and Exobiology Potential of Icy Satellites of the Giant Planets

NASA Astrophysics Data System (ADS)

Simakov, M. B.

2017-05-01

All giant planets of the Solar system have a big number of satellites. A small part of them consist very large bodies, quite comparable to planets of terrestrial type, but including very significant share of water ice. Galileo spacecraft has given indications, primarily from magnetometer and gravity data, of the possibility that three of Jupiter's four large moons, Europa, Ganymede and Callisto have internal oceans. Formation of such satellites is a natural phenomenon, and satellite systems definitely should exist at extrasolar planets. The most recent models of the icy satellites interior lead to the conclusion that a substantial liquid layer exists today under relatively thin ice cover inside. The putative internal water ocean provide some exobiological niches on these bodies. We can see all conditions needed for origin and evolution of biosphere - liquid water, complex organic chemistry and energy sources for support of biological processes - are on the moons. The existing of liquid water ocean within icy world can be consequences of the physical properties of water ice, and they neither require the addition of antifreeze substances nor any other special conditions. On Earth life exists in all niches where water exists in liquid form for at least a portion of the year. Possible metabolic processes, such as nitrate/nitrite reduction, sulfate reduction and methanogenesis could be suggested for internal oceans of Titan and Jovanian satellites. Excreted products of the primary chemoautotrophic organisms could serve as a source for other types of microorganisms (heterotrophes). Subglacial life may be widespread among such planetary bodies as satellites of extrasolar giant planets, detected in our Galaxy.

The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis

DOE PAGES

Dmytrenko, Oleg; Russell, Shelbi L.; Loo, Wesley T.; ...

2014-10-23

Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the abilitymore » to maintain it under laboratory conditions. Here, to better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. In conclusion, the physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle.« less

Geometry and lithofacies of coarse-grained injectites and extrudites in a late Pliocene trench-slope basin on the southern Boso Peninsula, Japan

NASA Astrophysics Data System (ADS)

Ito, Makoto; Ishimoto, Sakumi; Ito, Kento; Kotake, Nobuhiro

2016-10-01

This study investigates the geometry and internal structures of coarse- to very coarse-grained volcanic sandstones and volcanic breccias with many siltstone clasts (interpreted to be sill-like injectites and extrudites) occurring in an upper Pliocene trench-slope basin succession on the southern Boso Peninsula, Japan. The injectites occur in the uppermost Shiramazu Formation, and pinch out laterally into siltstone-dominated deposits of the Mera Formation. Their thicknesses vary from a few centimeters to 2 m. The basal and upper contacts of the injectites with host muddy deposits are sharp and/or erosional, and are locally discordant with the bedding of the host deposits. Siltstone clasts, which were ripped up or ripped down from the host muddy deposits, are commonly incorporated into the injectites, although some siltstone clasts have geological ages older than those of the host deposits. Seven lithofacies have been identified in the injectites based on the internal structures. The combinations of internal structures are different from those of high-density turbidity current deposits and debrites, and suggest that injection was promoted by a combination of turbulent and laminar flow conditions. The extrudites show an overall convex-up geometry and possess lithological features similar to those of the injectites. They have been identified in the Rendaiji Conglomerate Member, which is encased in the Mera Formation, and which rests on the uppermost Shiramazu Formation. The extrudites are characterized by gently undulating waveforms that show upstream migration and climbing stacking patterns similar to the cross-sectional geometry of cyclic steps or upstream-migrating antidunes. The active eruption of solid-liquid mixtures onto the seafloor and sedimentary piles may have subsequently collapsed to produce supercritical high-density gravity currents down the flanks of a neptunian volcano. The injectites and extrudites locally contain Calyptogena shells and shell fragments, as well as fragments of carbonate concretions that exhibit low carbon isotopic ratios, suggesting that fluidization of the source sediments was triggered by a combination of seepage of cold methane-bearing water into the source sediments and seismic shaking. Volcaniclastic deposits older than the host muddy deposits are present in the trench-slope basin deposits and these are the likely source of the injectites and extrudites.

CONVENTIONAL VIDEOENDOSCOPY CAN IDENTIFY HELICOBACTER PYLORI GASTRITIS?

PubMed

Gomes, Alexandre; Skare, Thelma Larocca; Prestes, Manoel Alberto; Costa, Maiza da Silva; Petisco, Roberta Dombroski; Ramos, Gabriela Piovezani

2016-01-01

Studies with latest technologies such as endoscopy with magnification and chromoendoscopy showed that various endoscopic aspects are clearly related to infection by Helicobacter pylori (HP). The description of different patterns of erythema in gastric body under magnification of images revived interest in identifying these patterns by standard endoscopy. To validate the morphologic features of gastric mucosa related to H. pylori infection gastritis allowing predictability of their diagnosis as well as proper targeting biopsies. Prospective study of 339 consecutive patients with the standard videoendoscope image analysis were obtained, recorded and stored in a program database. These images were studied with respect to the presence or absence of H. pylori, diagnosed by rapid urease test and/or by histological analysis. Were studied: a) normal mucosa appearance; b) mucosal nodularity; c) diffuse nonspecific erythema or redness (with or without edema of folds and exudate) of antrum and body; d) mosaic pattern with focal area of hyperemia; e) erythema in streaks or bands (red streak); f) elevated (raised) erosion; g) flat erosions; h) fundic gland polyps. The main exclusion criteria were the use of drugs, HP pre-treatment and other entities that could affect results. Applying the exclusion criteria, were included 170 of the 339 patients, of which 52 (30.58%) were positive for HP and 118 negative. On the positive findings, the most associated with infection were: nodularity in the antrum (26.92%); presence of raised erosion (15.38%) and mosaic mucosa in the body (21.15%). On the negative group the normal appearance of the mucosa was 66.94%; erythema in streaks or bands in 9.32%; flat erosions 11.86%; and fundic gland polyps 11.86%. Endoscopic findings are useful in the predictability of the result and in directing biopsies. The most representative form of HP related gastritis was the nodularity of the antral mucosa. The raised erosion and mucosa in mosaic in the body are suggestive but not specific to the infection. The other forms were not conclusive of the presence of HP. Estudos com tecnologias mais recentes como endoscopia com magnificação e cromoscopia mostraram que vários aspectos endoscópicos estão claramente associados à infecção por Helicobacter pylori. A descrição de padrões diferenciados de enantema no corpo gástrico através da magnificação de imagens reavivou o interesse na identificação desses padrões pela endoscopia convencional. Validar os padrões morfológicos de mucosa gástrica usando videogastroendoscopia convencional relacionados à gastrite por infecção por Helicobacter pylori, permitindo previsibilidade do seu diagnóstico e o direcionamento de biópsias. Estudo prospectivo de 339 pacientes consecutivos com análise das imagens de videogastroendoscopia obtidas, gravadas e armazenadas em banco de dados. Estas imagens foram estudadas com relação à presença ou não do Helicobacter pylori diagnosticado por teste rápido de urease e/ou por pesquisa direta por estudo anatomopatológico. Foram estudados: a) aspecto normal da mucosa; b) nodularidade da mucosa; c) enantema inespecífico difuso de antro e corpo; d) enantema em mosaico ou salpicado; e) enantema em estrias ou faixas; f) erosões elevadas; g) erosões planas; h) pólipos de glândulas fúndicas. Os principais critérios de exclusão foram o uso de medicamentos, tratamento prévio de HP e outras entidades que pudessem interferir nos resultados. Aplicando os critérios de exclusão, incluíram-se 170 dos 339 pacientes sendo 52 (30,58%) positivos para Helicobacter pylori e 118 negativos. No grupo positivo os achados que mais se associaram com a infecção foram: nodularidade no antro (26,92%); presença de erosões elevadas (15,38%) e mucosa em mosaico no corpo (21,15%). No grupo negativo o aspecto normal da mucosa foi de 66,94%; enantema em estrias ou faixas em 9,32%; erosões planas em 11,86%; e pólipos de glândulas fúndicas 11,86%. Achados endoscópicos são úteis na previsibilidade de localização e direcionamento de biópsias na pesquisa do HP. A mais representativa forma de gastrite por HP foi o achado de nodularidade na mucosa antral. As erosões elevadas e mucosa em mosaico no corpo são sugestivas, mas não específicas da infecção. As demais formas não foram conclusivas da presença do HP.

Structure and Identification of a Pterin Dehydratase-like Protein as a Ribulose-bisphosphate Carboxylase/Oxygenase (RuBisCO) Assembly Factor in the α-Carboxysome*

PubMed Central

Wheatley, Nicole M.; Sundberg, Christopher D.; Gidaniyan, Soheil D.; Cascio, Duilio; Yeates, Todd O.

2014-01-01

Carboxysomes are proteinaceous bacterial microcompartments that increase the efficiency of the rate-limiting step in carbon fixation by sequestering reaction substrates. Typically, α-carboxysomes are genetically encoded as a single operon expressing the structural proteins and the encapsulated enzymes of the microcompartment. In addition, depending on phylogeny, as many as 13 other genes are found to co-occur near or within α-carboxysome operons. One of these genes codes for a protein with distant homology to pterin-4α-carbinolamine dehydratase (PCD) enzymes. It is present in all α-carboxysome containing bacteria and has homologs in algae and higher plants. Canonical PCDs play an important role in amino acid hydroxylation, a reaction not associated with carbon fixation. We determined the crystal structure of an α-carboxysome PCD-like protein from the chemoautotrophic bacterium Thiomonas intermedia K12, at 1.3-Å resolution. The protein retains a three-dimensional fold similar to canonical PCDs, although the prominent active site cleft present in PCD enzymes is disrupted in the α-carboxysome PCD-like protein. Using a cell-based complementation assay, we tested the PCD-like proteins from T. intermedia and two additional bacteria, and found no evidence for PCD enzymatic activity. However, we discovered that heterologous co-expression of the PCD-like protein from Halothiobacillus neapolitanus with RuBisCO and GroELS in Escherichia coli increased the amount of soluble, assembled RuBisCO recovered from cell lysates compared with co-expression of RuBisCO with GroELS alone. We conclude that this conserved PCD-like protein, renamed here α-carboxysome RuBisCO assembly factor (or acRAF), is a novel RuBisCO chaperone integral to α-carboxysome function. PMID:24459150

Structure and identification of a pterin dehydratase-like protein as a ribulose-bisphosphate carboxylase/oxygenase (RuBisCO) assembly factor in the α-carboxysome.

PubMed

Wheatley, Nicole M; Sundberg, Christopher D; Gidaniyan, Soheil D; Cascio, Duilio; Yeates, Todd O

2014-03-14

Carboxysomes are proteinaceous bacterial microcompartments that increase the efficiency of the rate-limiting step in carbon fixation by sequestering reaction substrates. Typically, α-carboxysomes are genetically encoded as a single operon expressing the structural proteins and the encapsulated enzymes of the microcompartment. In addition, depending on phylogeny, as many as 13 other genes are found to co-occur near or within α-carboxysome operons. One of these genes codes for a protein with distant homology to pterin-4α-carbinolamine dehydratase (PCD) enzymes. It is present in all α-carboxysome containing bacteria and has homologs in algae and higher plants. Canonical PCDs play an important role in amino acid hydroxylation, a reaction not associated with carbon fixation. We determined the crystal structure of an α-carboxysome PCD-like protein from the chemoautotrophic bacterium Thiomonas intermedia K12, at 1.3-Å resolution. The protein retains a three-dimensional fold similar to canonical PCDs, although the prominent active site cleft present in PCD enzymes is disrupted in the α-carboxysome PCD-like protein. Using a cell-based complementation assay, we tested the PCD-like proteins from T. intermedia and two additional bacteria, and found no evidence for PCD enzymatic activity. However, we discovered that heterologous co-expression of the PCD-like protein from Halothiobacillus neapolitanus with RuBisCO and GroELS in Escherichia coli increased the amount of soluble, assembled RuBisCO recovered from cell lysates compared with co-expression of RuBisCO with GroELS alone. We conclude that this conserved PCD-like protein, renamed here α-carboxysome RuBisCO assembly factor (or acRAF), is a novel RuBisCO chaperone integral to α-carboxysome function.

The Diverse AAA+ Machines that Repair Inhibited Rubisco Active Sites

PubMed Central

Mueller-Cajar, Oliver

2017-01-01

Gaseous carbon dioxide enters the biosphere almost exclusively via the active site of the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco). This highly conserved catalyst has an almost universal propensity to non-productively interact with its substrate ribulose 1,5-bisphosphate, leading to the formation of dead-end inhibited complexes. In diverse autotrophic organisms this tendency has been counteracted by the recruitment of dedicated AAA+ (ATPases associated with various cellular activities) proteins that all use the energy of ATP hydrolysis to remodel inhibited Rubisco active sites leading to release of the inhibitor. Three evolutionarily distinct classes of these Rubisco activases (Rcas) have been discovered so far. Green and red-type Rca are mostly found in photosynthetic eukaryotes of the green and red plastid lineage respectively, whereas CbbQO is associated with chemoautotrophic bacteria. Ongoing mechanistic studies are elucidating how the various motors are utilizing both similar and contrasting strategies to ultimately perform their common function of cracking the inhibited Rubisco active site. The best studied mechanism utilized by red-type Rca appears to involve transient threading of the Rubisco large subunit C-terminal peptide, reminiscent of the action performed by Clp proteases. As well as providing a fascinating example of convergent molecular evolution, Rca proteins can be considered promising crop-improvement targets. Approaches aiming to replace Rubisco in plants with improved enzymes will need to ensure the presence of a compatible Rca protein. The thermolability of the Rca protein found in crop plants provides an opportunity to fortify photosynthesis against high temperature stress. Photosynthesis also appears to be limited by Rca when light conditions are fluctuating. Synthetic biology strategies aiming to enhance the autotrophic CO2 fixation machinery will need to take into consideration the requirement for Rubisco activases as well as their properties. PMID:28580359

Microbial community and nitrogen cycling shift with snowmelt in high-elevation barren soils of Mount Rainier National Park

NASA Astrophysics Data System (ADS)

Simpson, A.; Zabowski, D.

2015-12-01

Climate change and nutrient deposition have the potential to accelerate soil formation in high-elevation sediments recently exposed by glacier or snow melt. This process has implications not only for ecosystem formation on Earth but for the formation of Earth-like ecosystems on other planets and icy moons. Research into microbial communities shifting from subnival to mesotrophic conditions has mainly focused on changes on respiration and biomass, and is generally limited to one or two well-studied geographical locations. In particular, more information is needed on microbial shifts in snow-covered volcanic sediments, which may prove the closest analog to the most 'habitable' non-terrestrial environments for Earth microorganisms. We sampled in volcanic soil and sediment along gradients of elevation and snowmelt - dry soil, moist soil next to snowpack, and soil underneath snowpack - at the Muir Snowfields at Mount Rainier National Park, in order to investigate changes in carbon and nitrogen compounds, microbial diversity and gene expression. Initial results show a decrease in available ammonium and increase in microbial biomass carbon in exposed sediment with increasing soil moisture, and a sharp decrease in microbial C:N ratios after snowmelt and drying. Available/labile organic carbon and organic nitrogen decrease strongly with elevation, while microbial biomass carbon and nitrogen and mineral nitrogen compounds show no change with elevation. Though gene expression data is needed for confirmation, we hypothesize that these snowfields receive strong wind-borne deposits of carbon and nitrogen but that chemoautotrophic communities under semi-permanent snowpack do not shift to more mesotrophic communities until after exposed sediment has already begun to desiccate, limiting soil formation.

Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave.

PubMed

Ortiz, Marianyoly; Legatzki, Antje; Neilson, Julia W; Fryslie, Brandon; Nelson, William M; Wing, Rod A; Soderlund, Carol A; Pryor, Barry M; Maier, Raina M

2014-02-01

Carbonate caves represent subterranean ecosystems that are largely devoid of phototrophic primary production. In semiarid and arid regions, allochthonous organic carbon inputs entering caves with vadose-zone drip water are minimal, creating highly oligotrophic conditions; however, past research indicates that carbonate speleothem surfaces in these caves support diverse, predominantly heterotrophic prokaryotic communities. The current study applied a metagenomic approach to elucidate the community structure and potential energy dynamics of microbial communities, colonizing speleothem surfaces in Kartchner Caverns, a carbonate cave in semiarid, southeastern Arizona, USA. Manual inspection of a speleothem metagenome revealed a community genetically adapted to low-nutrient conditions with indications that a nitrogen-based primary production strategy is probable, including contributions from both Archaea and Bacteria. Genes for all six known CO2-fixation pathways were detected in the metagenome and RuBisCo genes representative of the Calvin-Benson-Bassham cycle were over-represented in Kartchner speleothem metagenomes relative to bulk soil, rhizosphere soil and deep-ocean communities. Intriguingly, quantitative PCR found Archaea to be significantly more abundant in the cave communities than in soils above the cave. MEtaGenome ANalyzer (MEGAN) analysis of speleothem metagenome sequence reads found Thaumarchaeota to be the third most abundant phylum in the community, and identified taxonomic associations to this phylum for indicator genes representative of multiple CO2-fixation pathways. The results revealed that this oligotrophic subterranean environment supports a unique chemoautotrophic microbial community with potentially novel nutrient cycling strategies. These strategies may provide key insights into other ecosystems dominated by oligotrophy, including aphotic subsurface soils or aquifers and photic systems such as arid deserts.

Methane-Carbon Flow into the Benthic Food Web at Cold Seeps – A Case Study from the Costa Rica Subduction Zone

PubMed Central

Niemann, Helge; Linke, Peter; Knittel, Katrin; MacPherson, Enrique; Boetius, Antje; Brückmann, Warner; Larvik, Gaute; Wallmann, Klaus; Schacht, Ulrike; Omoregie, Enoma; Hilton, David; Brown, Kevin; Rehder, Gregor

2013-01-01

Cold seep ecosystems can support enormous biomasses of free-living and symbiotic chemoautotrophic organisms that get their energy from the oxidation of methane or sulfide. Most of this biomass derives from animals that are associated with bacterial symbionts, which are able to metabolize the chemical resources provided by the seeping fluids. Often these systems also harbor dense accumulations of non-symbiotic megafauna, which can be relevant in exporting chemosynthetically fixed carbon from seeps to the surrounding deep sea. Here we investigated the carbon sources of lithodid crabs (Paralomis sp.) feeding on thiotrophic bacterial mats at an active mud volcano at the Costa Rica subduction zone. To evaluate the dietary carbon source of the crabs, we compared the microbial community in stomach contents with surface sediments covered by microbial mats. The stomach content analyses revealed a dominance of epsilonproteobacterial 16S rRNA gene sequences related to the free-living and epibiotic sulfur oxidiser Sulfurovum sp. We also found Sulfurovum sp. as well as members of the genera Arcobacter and Sulfurimonas in mat-covered surface sediments where Epsilonproteobacteria were highly abundant constituting 10% of total cells. Furthermore, we detected substantial amounts of bacterial fatty acids such as i-C15∶0 and C17∶1ω6c with stable carbon isotope compositions as low as −53‰ in the stomach and muscle tissue. These results indicate that the white microbial mats at Mound 12 are comprised of Epsilonproteobacteria and that microbial mat-derived carbon provides an important contribution to the crab's nutrition. In addition, our lipid analyses also suggest that the crabs feed on other 13C-depleted organic matter sources, possibly symbiotic megafauna as well as on photosynthetic carbon sources such as sedimentary detritus. PMID:24116017

Reservoir-Scale Biological Community Response to Trace Element Additions in a Northern Montana Oil Field

NASA Astrophysics Data System (ADS)

Connors, D. E.; Bradfish, J.; DeBruyn, R. P.; Zemetra, J.; Mitchell, H.

2017-12-01

In subsurface oil bearing formations, microbial growth and metabolism is restricted due to a lack of elements other than carbon, hydrogen, and oxygen required for cell structure and as cofactors. A chemical treatment that adds these elements back into the formation was deployed into an oil reservoir in Northern Montana, with the intent of increasing biogenic methane generation. Samples of water from producing wells in the reservoir were collected anaerobically, and analyzed for geochemical content, and cells from the water were collected and analyzed via 16S rRNA gene DNA sequencing to determine the makeup of the microbial community over the course of twelve months of treatment, and for two years after. Prior to chemical treatment, this reservoir was depleted in elements required for enzyme co-factors in the methanogenesis metabolic pathway (Co, Mo, Ni, W, Zn) as well as nitrogen and phosphorus. Most the microbial community was composed of chemoheterotrophic bacteria associated with the biodegradation of large carbon molecules, with a small community of acetoclastic methanogens. During and after additions of the depleted elements, the metabolism of the community in the reservoir shifted towards chemoautotrophs and hydrogenotrophic methanogens, and the cell density increased. After treatment was ended, cell counts stabilized at a new equilibrium concentration, and the autotrophic metabolism was maintained. The pre-treatment community was dependent on energy input from solubilized oil molecules, whereas the post-treatment community more effectively utilized dissolved organics and carbon dioxide as carbon sources for fixation and respiration. This study demonstrates the capability of microbial communities to rapidly reorganize in the environment when provided with an influx of the elements required for growth and metabolism.

Genetic Connectivity between North and South Mid-Atlantic Ridge Chemosynthetic Bivalves and Their Symbionts

PubMed Central

van der Heijden, Karina; Petersen, Jillian M.; Dubilier, Nicole; Borowski, Christian

2012-01-01

Transform faults are geological structures that interrupt the continuity of mid-ocean ridges and can act as dispersal barriers for hydrothermal vent organisms. In the equatorial Atlantic Ocean, it has been hypothesized that long transform faults impede gene flow between the northern and the southern Mid-Atlantic Ridge (MAR) and disconnect a northern from a southern biogeographic province. To test if there is a barrier effect in the equatorial Atlantic, we examined phylogenetic relationships of chemosynthetic bivalves and their bacterial symbionts from the recently discovered southern MAR hydrothermal vents at 5°S and 9°S. We examined Bathymodiolus spp. mussels and Abyssogena southwardae clams using the mitochondrial cytochrome c oxidase subunit I (COI) gene as a phylogenetic marker for the hosts and the bacterial 16S rRNA gene as a marker for the symbionts. Bathymodiolus spp. from the two southern sites were genetically divergent from the northern MAR species B. azoricus and B. puteoserpentis but all four host lineages form a monophyletic group indicating that they radiated after divergence from their northern Atlantic sister group, the B. boomerang species complex. This suggests dispersal of Bathymodiolus species from north to south across the equatorial belt. 16S rRNA genealogies of chemoautotrophic and methanotrophic symbionts of Bathymodiolus spp. were inconsistent and did not match the host COI genealogy indicating disconnected biogeography patterns. The vesicomyid clam Abyssogena southwardae from 5°S shared an identical COI haplotype with A. southwardae from the Logatchev vent field on the northern MAR and their symbionts shared identical 16S phylotypes, suggesting gene flow across the Equator. Our results indicate genetic connectivity between the northern and southern MAR and suggest that a strict dispersal barrier does not exist. PMID:22792208

Methane-carbon flow into the benthic food web at cold seeps--a case study from the Costa Rica subduction zone.

PubMed

Niemann, Helge; Linke, Peter; Knittel, Katrin; MacPherson, Enrique; Boetius, Antje; Brückmann, Warner; Larvik, Gaute; Wallmann, Klaus; Schacht, Ulrike; Omoregie, Enoma; Hilton, David; Brown, Kevin; Rehder, Gregor

2013-01-01

Cold seep ecosystems can support enormous biomasses of free-living and symbiotic chemoautotrophic organisms that get their energy from the oxidation of methane or sulfide. Most of this biomass derives from animals that are associated with bacterial symbionts, which are able to metabolize the chemical resources provided by the seeping fluids. Often these systems also harbor dense accumulations of non-symbiotic megafauna, which can be relevant in exporting chemosynthetically fixed carbon from seeps to the surrounding deep sea. Here we investigated the carbon sources of lithodid crabs (Paralomis sp.) feeding on thiotrophic bacterial mats at an active mud volcano at the Costa Rica subduction zone. To evaluate the dietary carbon source of the crabs, we compared the microbial community in stomach contents with surface sediments covered by microbial mats. The stomach content analyses revealed a dominance of epsilonproteobacterial 16S rRNA gene sequences related to the free-living and epibiotic sulfur oxidiser Sulfurovum sp. We also found Sulfurovum sp. as well as members of the genera Arcobacter and Sulfurimonas in mat-covered surface sediments where Epsilonproteobacteria were highly abundant constituting 10% of total cells. Furthermore, we detected substantial amounts of bacterial fatty acids such as i-C15∶0 and C17∶1ω6c with stable carbon isotope compositions as low as -53‰ in the stomach and muscle tissue. These results indicate that the white microbial mats at Mound 12 are comprised of Epsilonproteobacteria and that microbial mat-derived carbon provides an important contribution to the crab's nutrition. In addition, our lipid analyses also suggest that the crabs feed on other (13)C-depleted organic matter sources, possibly symbiotic megafauna as well as on photosynthetic carbon sources such as sedimentary detritus.

Measurement of Fe2+ ion by coulometry method at incubation of Thiobacillus ferrooxidans.

PubMed

Tsuda, I; Kato, K; Nozaki, K

1996-12-01

Thiobacillus ferrooxidans is a chemoautotrophic bacterium that is capable of using Fe2+ oxidation by O2 as the sole source of energy for growth and CO2 fixation. The idea of the solar bacterial biomass farm by using of this bacterium is proposed. The incubation experiment of these bacteria was carried out, and the 9K culture medium as the standard medium for T. ferrooxidans was used. The measurement of Fe2+ in the growth stage was carried out as the first step of the experiments to clarify the possibility of this system. The items of measurement were Fe2+ ion density, pH of the medium, bacterium density and quantity of total organic carbon (TOC). The density of Fe2+ ion in the medium was measured by coulometry method. This method has the following advantage, high accuracy (<1%), easy operation, short measurement time (a few minutes) and small sample quantity (about 0.1 ml). The experimental results show that the Fe 2+ ion density is measured as same as the accuracy of pH measurement. At the final stage of the growth, the pH decreased due to the generation of the iron hydroxide (Fe(OH)3). The bacterium density and TOC slightly increased after that Fe2+ runs short. This result shows that the CO2 fixation speed is slower than Fe2+ oxidation speed. It is shown by the experiment that the growth limit of T. ferrooxidans is caused by the disappearance of the Fe2+ ion. It may be possible that the bacterium density increases by the continuous supply of Fe2+ ion.

Insights into the Structure and Metabolic Function of Microbes That Shape Pelagic Iron-Rich Aggregates (“Iron Snow”)

PubMed Central

Lu, Shipeng; Chourey, Karuna; Reiche, Marco; Nietzsche, Sandor; Shah, Manesh B.; Neu, Thomas R.; Hettich, Robert L.

2013-01-01

Microbial ferrous iron [Fe(II)] oxidation leads to the formation of iron-rich macroscopic aggregates (“iron snow”) at the redoxcline in a stratified lignite mine lake in east-central Germany. We aimed to identify the abundant Fe-oxidizing and Fe-reducing microorganisms likely to be involved in the formation and transformation of iron snow present in the redoxcline in two basins of the lake that differ in their pH values. Nucleic acid- and lipid-stained microbial cells of various morphologies detected by confocal laser scanning microscopy were homogeneously distributed in all iron snow samples. The dominant iron mineral appeared to be schwertmannite, with shorter needles in the northern than in the central basin samples. Total bacterial 16S rRNA gene copies ranged from 5.0 × 108 copies g (dry weight)−1 in the acidic central lake basin (pH 3.3) to 4.0 × 1010 copies g (dry weight)−1 in the less acidic (pH 5.9) northern basin. Total RNA-based quantitative PCR assigned up to 61% of metabolically active microbial communities to Fe-oxidizing- and Fe-reducing-related bacteria, indicating that iron metabolism was an important metabolic strategy. Molecular identification of abundant groups suggested that iron snow surfaces were formed by chemoautotrophic iron oxidizers, such as Acidimicrobium, Ferrovum, Acidithiobacillus, Thiobacillus, and Chlorobium, in the redoxcline and were rapidly colonized by heterotrophic iron reducers, such as Acidiphilium, Albidiferax-like, and Geobacter-like groups. Metaproteomics yielded 283 different proteins from northern basin iron snow samples, and protein identification provided a glimpse into some of their in situ metabolic processes, such as primary production (CO2 fixation), respiration, motility, and survival strategies. PMID:23645202

Insights into the structure and metabolic function of microbes that shape pelagic iron-rich aggregates ("iron snow").

PubMed

Lu, Shipeng; Chourey, Karuna; Reiche, Marco; Nietzsche, Sandor; Shah, Manesh B; Neu, Thomas R; Hettich, Robert L; Küsel, Kirsten

2013-07-01

Microbial ferrous iron [Fe(II)] oxidation leads to the formation of iron-rich macroscopic aggregates ("iron snow") at the redoxcline in a stratified lignite mine lake in east-central Germany. We aimed to identify the abundant Fe-oxidizing and Fe-reducing microorganisms likely to be involved in the formation and transformation of iron snow present in the redoxcline in two basins of the lake that differ in their pH values. Nucleic acid- and lipid-stained microbial cells of various morphologies detected by confocal laser scanning microscopy were homogeneously distributed in all iron snow samples. The dominant iron mineral appeared to be schwertmannite, with shorter needles in the northern than in the central basin samples. Total bacterial 16S rRNA gene copies ranged from 5.0 × 10(8) copies g (dry weight)(-1) in the acidic central lake basin (pH 3.3) to 4.0 × 10(10) copies g (dry weight)(-1) in the less acidic (pH 5.9) northern basin. Total RNA-based quantitative PCR assigned up to 61% of metabolically active microbial communities to Fe-oxidizing- and Fe-reducing-related bacteria, indicating that iron metabolism was an important metabolic strategy. Molecular identification of abundant groups suggested that iron snow surfaces were formed by chemoautotrophic iron oxidizers, such as Acidimicrobium, Ferrovum, Acidithiobacillus, Thiobacillus, and Chlorobium, in the redoxcline and were rapidly colonized by heterotrophic iron reducers, such as Acidiphilium, Albidiferax-like, and Geobacter-like groups. Metaproteomics yielded 283 different proteins from northern basin iron snow samples, and protein identification provided a glimpse into some of their in situ metabolic processes, such as primary production (CO2 fixation), respiration, motility, and survival strategies.

The importance of methane and thiosulfate in the metabolism of the bacterial symbionts of two deep-sea mussels

USGS Publications Warehouse

Fisher, C.R.; Childress, J.J.; Oremland, R.S.; Bidigare, R.R.

1987-01-01

Undescribed hydrocarbon-seep mussels were collected from the Louisiana Slope, Gulf of Mexico, during March 1986, and the ultrastructure of their gills was examined and compared to Bathymodiolus thermophilus, a mussel collected from the deep-sea hydrothermal vents on the Gala??pagos Rift in March 1985. These closely related mytilids both contain abundant symbiotic bacteria in their gills. However, the bacteria from the two species are distinctly different in both morphology and biochemistry, and are housed differently within the gills of the two mussels. The symbionts from the seep mussel are larger than the symbionts from B. thermophilus and, unlike the latter, contain stacked intracytoplasmic membranes. In the seep mussel three or fewer symbionts appear to be contained in each host-cell vacuole, while in B. thermophilus there are often more than twenty bacteria visible in a single section through a vacuole. The methanotrophic nature of the seep-mussel symbionts was confirmed in 14C-methane uptake experiments by the appearance of label in both CO2 and acid-stable, non-volatile, organic compounds after a 3 h incubation of isolated gill tissue. Furthermore, methane consumption was correlated with methanol dehydrogenase activity in isolated gill tissue. Activity of ribulose-1,5-biphosphate (RuBP) carboxylase and 14CO2 assimilation studies indicate the presence of either a second type of symbiont or contaminating bacteria on the gills of freshly captured seep mussels. A reevaluation of the nutrition of the symbionts in B. thermophilus indicates that while the major symbiont is not a methanotroph, its status as a sulfur-oxidizing chemoautotroph, as has been suggested previously, is far from proven. ?? 1987 Springer-Verlag.

Ammonia-oxidizing archaea versus bacteria in two soil aquifer treatment systems.

PubMed

Ding, Kun; Wen, Xianghua; Li, Yuyang; Shen, Bo; Zhang, Bing

2015-02-01

So far, the contribution of ammonia-oxidizing archaea (AOA) to ammonia oxidation in wastewater treatment processes has not been well understood. In this study, two soil aquifer treatment (SATs) systems were built up to treat synthetic domestic wastewater (column 1) and secondary effluent (column 4), accomplishing an average of 95% ammonia removal during over 550 days of operation. Except at day 322, archaeal amoA genes always outnumbered bacterial amoA genes in both SATs as determined by using quantitative polymerase chain reaction (q-PCR). The ratios of archaeal amoA to 16S rRNA gene averaged at 0.70 ± 0.56 and 0.82 ± 0.62 in column 1 and column 4, respectively, indicating that all the archaea could be AOA carrying amoA gene in the SATs. The results of MiSeq-pyrosequencing targeting on archaeal and bacterial 16S rRNA genes with the primer pair of modified 515R/806R indicated that Nitrososphaera cluster affiliated with thaumarchaeal group I.1b was the dominant AOA species, while Nitrosospira cluster was the dominant ammonia-oxidizing bacteria (AOB). The statistical analysis showed significant relationship between AOA abundance (compared to AOB abundance) and inorganic and total nitrogen concentrations. Based on the mathematical model calculation for microbial growth, AOA had much greater capacity of ammonia oxidation as compared to the specific influent ammonia loading for AOA in the SATs, implying that a small fraction of the total AOA would actively work to oxidize ammonia chemoautotrophically whereas most of AOA would exhibit some level of functional redundancy. These results all pointed that AOA involved in microbial ammonia oxidation in the SATs.

Bacterial sulfite dehydrogenases in organotrophic metabolism: separation and identification in Cupriavidus necator H16 and in Delftia acidovorans SPH-1.

PubMed

Denger, Karin; Weinitschke, Sonja; Smits, Theo H M; Schleheck, David; Cook, Alasdair M

2008-01-01

The utilization of organosulfonates as carbon sources by aerobic or nitrate-reducing bacteria usually involves a measurable, uncharacterized sulfite dehydrogenase. This is tacitly assumed to be sulfite : ferricytochrome-c oxidoreductase [EC 1.8.2.1], despite negligible interaction with (eukaryotic) cytochrome c: the enzyme is assayed at high specific activity with ferricyanide as electron acceptor. Purified periplasmic sulfite dehydrogenases (SorAB, SoxCD) are known from chemoautotrophic growth and are termed 'sulfite oxidases' by bioinformatic services. The catalytic unit (SorA, SoxC; termed 'sulfite oxidases' cd02114 and cd02113, respectively) binds a molybdenum-cofactor (Moco), and involves a cytochrome c (SorB, SoxD) as electron acceptor. The genomes of several bacteria that express a sulfite dehydrogenase during heterotrophic growth contain neither sorAB nor soxCD genes; others contain at least four paralogues, for example Cupriavidus necator H16, which is known to express an inducible sulfite dehydrogenase during growth with taurine (2-aminoethanesulfonate). This soluble enzyme was enriched 320-fold in four steps. The 40 kDa protein (denatured) had an N-terminal amino acid sequence which started at position 42 of the deduced sequence of H16_B0860 (termed 'sulfite oxidase' cd02114), which we named SorA. The neighbouring gene is an orthologue of sorB, and the sorAB genes were co-transcribed. Cell fractionation showed SorA to be periplasmic. The corresponding enzyme in Delftia acidovorans SPH-1 was enriched 270-fold, identified as Daci_0055 (termed 'sulfite oxidase' cd02110) and has a cytochrome c encoded downstream. We presume, from genomic data for bacteria and archaea, that there are several subgroups of sulfite dehydrogenases, which all contain a Moco, and transfer electrons to a specific cytochrome c.

Abundance and distribution of archaeal acetyl-CoA/propionyl-CoA carboxylase genes indicative for putatively chemoautotrophic Archaea in the tropical Atlantic's interior.

PubMed

Bergauer, Kristin; Sintes, Eva; van Bleijswijk, Judith; Witte, Harry; Herndl, Gerhard J

2013-06-01

Recently, evidence suggests that dark CO2 fixation in the pelagic realm of the ocean does not only occur in the suboxic and anoxic water bodies but also in the oxygenated meso- and bathypelagic waters of the North Atlantic. To elucidate the significance and phylogeny of the key organisms mediating dark CO2 fixation in the tropical Atlantic, we quantified functional genes indicative for CO2 fixation. We used a Q-PCR-based assay targeting the bifunctional acetyl-CoA/propionyl-CoA carboxylase (accA subunit), a key enzyme powering inter alia the 3-hydroxypropionate/4-hydroxybutyrate cycle (HP/HB) and the archaeal ammonia monooxygenase (amoA). Quantification of accA-like genes revealed a consistent depth profile in the upper mesopelagial with increasing gene abundances from subsurface layers towards the oxygen minimum zone (OMZ), coinciding with an increase in archaeal amoA gene abundance. Gene abundance profiles of metabolic marker genes (accA, amoA) were correlated with thaumarchaeal 16S rRNA gene abundances as well as CO2 fixation rates to link the genetic potential to actual rate measurements. AccA gene abundances correlated with archaeal amoA gene abundance throughout the water column (r(2)  = 0.309, P < 0.0001). Overall, a substantial genetic predisposition of CO2 fixation was present in the dark realm of the tropical Atlantic in both Archaea and Bacteria. Hence, dark ocean CO2 fixation might be more widespread among prokaryotes inhabiting the oxygenated water column of the ocean's interior than hitherto assumed. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Twentieth-century decline of large-diameter trees in Yosemite National Park, California, USA

USGS Publications Warehouse

Lutz, J.A.; van Wagtendonk, J.W.; Franklin, J.F.

2009-01-01

Studies of forest change in western North America often focus on increased densities of small-diameter trees rather than on changes in the large tree component. Large trees generally have lower rates of mortality than small trees and are more resilient to climate change, but these assumptions have rarely been examined in long-term studies. We combined data from 655 historical (1932-1936) and 210 modern (1988-1999) vegetation plots to examine changes in density of large-diameter trees in Yosemite National Park (3027 km2). We tested the assumption of stability for large-diameter trees, as both individual species and communities of large-diameter trees. Between the 1930s and 1990s, large-diameter tree density in Yosemite declined 24%. Although the decrease was apparent in all forest types, declines were greatest in subalpine and upper montane forests (57.0% of park area), and least in lower montane forests (15.3% of park area). Large-diameter tree densities of 11 species declined while only 3 species increased. Four general patterns emerged: (1) Pinus albicaulis, Quercus chrysolepis, and Quercus kelloggii had increases in density of large-diameter trees occur throughout their ranges; (2) Pinus jeffreyi, Pinus lambertiana, and Pinus ponderosa, had disproportionately larger decreases in large-diameter tree densities in lower-elevation portions of their ranges; (3) Abies concolor and Pinus contorta, had approximately uniform decreases in large-diameter trees throughout their elevational ranges; and (4) Abies magnifica, Calocedrus decurrens, Juniperus occidentalis, Pinus monticola, Pseudotsuga menziesii, and Tsuga mertensiana displayed little or no change in large-diameter tree densities. In Pinus ponderosa-Calocedrus decurrens forests, modern large-diameter tree densities were equivalent whether or not plots had burned since 1936. However, in unburned plots, the large-diameter trees were predominantly A. concolor, C. decurrens, and Q. chrysolepis, whereas P. ponderosa dominated the large-diameter component of burned plots. Densities of large-diameter P. ponderosa were 8.1 trees ha-1 in plots that had experienced fire, but only 0.5 trees ha-1 in plots that remained unburned. ?? 2009 Elsevier B.V. All rights reserved.

The radiation resistance and cobalt biosorption activity of yeast strains isolated from the Lanyu low-level radioactive waste repository in Taiwan.

PubMed

Li, Chia-Chin; Chung, Hsiao-Ping; Wen, Hsiao-Wei; Chang, Ching-Tu; Wang, Ya-Ting; Chou, Fong-In

2015-08-01

The ubiquitous nature of microbes has made them the pioneers in radionuclides adsorption and transport. In this study, the radiation resistance and nuclide biosorption capacity of microbes isolated from the Lanyu low-level radioactive waste (LLRW) repository in Taiwan was assessed, the evaluation of the possibility of using the isolated strain as biosorbents for (60)Co and Co (II) from contaminated aqueous solution and the potential impact on radionuclides release. The microbial content of solidified waste and broken fragments of containers at the Lanyu LLRW repository reached 10(5) CFU/g. Two yeast strains, Candida guilliermondii (CT1) and Rhodotorula calyptogenae (RT1) were isolated. The radiation dose necessary to reduce the microbial count by one log cycle of CT1 and RT1 was 2.1 and 0.8 kGy, respectively. Both CT1 and RT1 can grow under a radiation field with dose rate of 6.8 Gy/h, about 100 times higher than that on the surface of the LLRW container in Lanyu repository. CT1 and RT1 had the maximum (60)Co biosorption efficiency of 99.7 ± 0.1% and 98.3 ± 0.2%, respectively in (60)Co aqueous solution (700 Bq/mL), and the (60)Co could stably retained for more than 30 days in CT 1. Nearly all of the Co was absorbed and reached equilibrium within 1 h by CT1 and RT1 in the 10 μg/g Co (II) aqueous solution. Biosorption efficiency test showed almost all of the Co (II) was adsorbed by CT1 in 20 μg/g Co (II) aqueous solution, the efficiency of biosorption by RT1 in 10 μg/g of Co (II) was lower. The maximum Co (II) sorption capacity of CT1 and RT1 was 5324.0 ± 349.0 μg/g (dry wt) and 3737.6 ± 86.5 μg/g (dry wt), respectively, in the 20 μg/g Co (II) aqueous solution. Experimental results show that microbial activity was high in the Lanyu LLRW repository in Taiwan. Two isolated yeast strains, CT1 and RT1 have high potential for use as biosorbents for (60)Co and Co (II) from contaminated aqueous solution, on the other hand, but may have the impact on radionuclides release from LLRW repository. Copyright © 2015 Elsevier Ltd. All rights reserved.

Developing a Long-Term Forest Gap Model to Predict the Behavior of California Pines, Oaks, and Cedars Under Climate Change and Other Disturbance Scenarios

NASA Astrophysics Data System (ADS)

Davis, S. L.; Moran, E.

2015-12-01

Many predictions about how trees will respond to climate change have been made, but these often rely on extrapolating into the future one of two extremes: purely correlative factors like climate, or purely physiological factors unique to a particular species or plant functional group. We are working towards a model that combines both phenotypic and genotypic traits to better predict responses of trees to climate change. We have worked to parameterize a neighborhood dynamics, individual tree forest-gap model called SORTIE-ND, using open data from both the USDA Forest Service Forest Inventory & Analysis (FIA) datasets in California and 30-yr old permanent plots established by the USGS. We generated individual species factors including stage-specific mortality and growth rates, and species-specific allometric equations for ten species, including Abies concolor, A. magnifica, Calocedrus decurrens, Pinus contorta, P. jeffreyi, P. lambertiana, P. monticola, P. ponderosa, and the two hardwoods Quercus chrysolepis and Q. kelloggii. During this process, we also developed two R packages to aid in parameter development for SORTIE-ND in other ecological systems. MakeMyForests is an R package that parses FIA datasets and calculates parameters based on the state averages of growth, light, and allometric parameters. disperseR is an R package that uses extensive plot data, with individual tree, sapling, and seedling measurements, to calculate finely tuned mortality and growth parameters for SORTIE-ND. Both are freely available on GitHub, and future updates will be available on CRAN. To validate the model, we withheld several plots from the 30-yr USGS data while calculating parameters. We tested for differences between the actual withheld data and the simulated forest data, in basal area, seedling density, seed dispersal, and species composition. The similarity of our model to the real system suggests that the model parameters we generated with our R packages accurately represent the system, and that our model can be extended to include changes in precipitation, temperature, and disturbance with very little manipulaton. We hope that our examples, R package development, and SORTIE-ND module development will enable other ecologists to utilize SORTIE-ND to predict changes in local and important ecoystems around the world.

Determinants of reproductive success in dominant pairs of clownfish: a boosted regression tree analysis.

PubMed

Buston, Peter M; Elith, Jane

2011-05-01

1. Central questions of behavioural and evolutionary ecology are what factors influence the reproductive success of dominant breeders and subordinate nonbreeders within animal societies? A complete understanding of any society requires that these questions be answered for all individuals. 2. The clown anemonefish, Amphiprion percula, forms simple societies that live in close association with sea anemones, Heteractis magnifica. Here, we use data from a well-studied population of A. percula to determine the major predictors of reproductive success of dominant pairs in this species. 3. We analyse the effect of multiple predictors on four components of reproductive success, using a relatively new technique from the field of statistical learning: boosted regression trees (BRTs). BRTs have the potential to model complex relationships in ways that give powerful insight. 4. We show that the reproductive success of dominant pairs is unrelated to the presence, number or phenotype of nonbreeders. This is consistent with the observation that nonbreeders do not help or hinder breeders in any way, confirming and extending the results of a previous study. 5. Primarily, reproductive success is negatively related to male growth and positively related to breeding experience. It is likely that these effects are interrelated because males that grow a lot have little breeding experience. These effects are indicative of a trade-off between male growth and parental investment. 6. Secondarily, reproductive success is positively related to female growth and size. In this population, female size is positively related to group size and anemone size, also. These positive correlations among traits likely are caused by variation in site quality and are suggestive of a silver-spoon effect. 7. Noteworthily, whereas reproductive success is positively related to female size, it is unrelated to male size. This observation provides support for the size advantage hypothesis for sex change: both individuals maximize their reproductive success when the larger individual adopts the female tactic. 8. This study provides the most complete picture to date of the factors that predict the reproductive success of dominant pairs of clown anemonefish and illustrates the utility of BRTs for analysis of complex behavioural and evolutionary ecology data. © 2011 The Authors. Journal of Animal Ecology © 2011 British Ecological Society.

Biotransformation of arsenic species by activated sludge and removal of bio-oxidised arsenate from wastewater by coagulation with ferric chloride.

PubMed

Andrianisa, Harinaivo Anderson; Ito, Ayumi; Sasaki, Atsushi; Aizawa, Jiro; Umita, Teruyuki

2008-12-01

The potential of activated sludge to catalyse bio-oxidation of arsenite [As(III)] to arsenate [As(V)] and bio-reduction of As(V) to As(III) was investigated. In batch experiments (pH 7, 25 degrees C) using activated sludge taken from a treatment plant receiving municipal wastewater non-contaminated with As, As(III) and As(V) were rapidly biotransformed to As(V) under aerobic condition and As(III) under anaerobic one without acclimatisation, respectively. Sub-culture of the activated sludge using a minimal liquid medium containing 100mg As(III)/L and no organic carbon source showed that aerobic arsenic-resistant bacteria were present in the activated sludge and one of the isolated bacteria was able to chemoautotrophically oxidise As(III) to As(V). Analysis of arsenic species in a full-scale oxidation ditch plant receiving As-contaminated wastewater revealed that both As(III) and As(V) were present in the influent, As(III) was almost completely oxidised to As(V) after supply of oxygen by the aerator in the oxidation ditch, As(V) oxidised was reduced to As(III) in the anaerobic zone in the ditch and in the return sludge pipe, and As(V) was the dominant species in the effluent. Furthermore, co-precipitation of As(V) bio-oxidised by activated sludge in the plant with ferric hydroxide was assessed by jar tests. It was shown that the addition of ferric chloride to mixed liquor as well as effluent achieved high removal efficiencies (>95%) of As and could decrease the residual total As concentrations in the supernatant from about 200 microg/L to less than 5 microg/L. It was concluded that a treatment process combining bio-oxidation with activated sludge and coagulation with ferric chloride could be applied as an alternative technology to treat As-contaminated wastewater.

Ferrous iron- and ammonium-rich diffuse vents support habitat-specific communities in a shallow hydrothermal field off the Basiluzzo Islet (Aeolian Volcanic Archipelago).

PubMed

Bortoluzzi, G; Romeo, T; La Cono, V; La Spada, G; Smedile, F; Esposito, V; Sabatino, G; Di Bella, M; Canese, S; Scotti, G; Bo, M; Giuliano, L; Jones, D; Golyshin, P N; Yakimov, M M; Andaloro, F

2017-09-01

Ammonium- and Fe(II)-rich fluid flows, known from deep-sea hydrothermal systems, have been extensively studied in the last decades and are considered as sites with high microbial diversity and activity. Their shallow-submarine counterparts, despite their easier accessibility, have so far been under-investigated, and as a consequence, much less is known about microbial communities inhabiting these ecosystems. A field of shallow expulsion of hydrothermal fluids has been discovered at depths of 170-400 meters off the base of the Basiluzzo Islet (Aeolian Volcanic Archipelago, Southern Tyrrhenian Sea). This area consists predominantly of both actively diffusing and inactive 1-3 meters-high structures in the form of vertical pinnacles, steeples and mounds covered by a thick orange to brown crust deposits hosting rich benthic fauna. Integrated morphological, mineralogical, and geochemical analyses revealed that, above all, these crusts are formed by ferrihydrite-type Fe 3+ oxyhydroxides. Two cruises in 2013 allowed us to monitor and sampled this novel ecosystem, certainly interesting in terms of shallow-water iron-rich site. The main objective of this work was to characterize the composition of extant communities of iron microbial mats in relation to the environmental setting and the observed patterns of macrofaunal colonization. We demonstrated that iron-rich deposits contain complex and stratified microbial communities with a high proportion of prokaryotes akin to ammonium- and iron-oxidizing chemoautotrophs, belonging to Thaumarchaeota, Nitrospira, and Zetaproteobacteria. Colonizers of iron-rich mounds, while composed of the common macrobenthic grazers, predators, filter-feeders, and tube-dwellers with no representatives of vent endemic fauna, differed from the surrounding populations. Thus, it is very likely that reduced electron donors (Fe 2+ and NH 4 + ) are important energy sources in supporting primary production in microbial mats, which form a habitat-specific trophic base of the whole Basiluzzo hydrothermal ecosystem, including macrobenthic fauna. © 2017 John Wiley & Sons Ltd.

[Rhodobaculum claviforme gen. nov., sp. nov., a New Alkaliphilic Nonsulfur Purple Bacterium].

PubMed

Bryantseva, I A; Gaisin, V A; Gorlenko, V M

2015-01-01

Two alkaliphilic strains of nonsulfur purple bacteria (NPB), B7-4 and B8-2, were isolated from southeast Siberia moderately saline alkaline steppe lakes with pH values above 9.0. The isolates were motile, polymorphous cells (from short rods to long spindly cells) 2.0-3.2 x 9.6-20.0 μm. Intracellular membranes of vesicular type were mostly located at the cell periphery. The microorganisms contained bacteriochlorophyll a and carotenoids of the spheroidene and spirilloxanthin series. The photosynthetic apparatus was represented by LH2 and LH1 light-harvesting complexes. In the presence of organic compounds, the strains grew aerobically in the dark or anaerobically in the light. Capacity for photo- and chemoautotrophic growth was not detected. The cbbl gene encoding RuBisCO was not revealed. Optimal growth of both strains occurred at 2% NaCl (range from 0.5 to 4%), pH 8.0-8.8 (range from 7.5 to 9.7), and 25-35 degrees C. The DNA G+C content was 67.6-69.8 mol %. Pairwise comparison of the nucleotides of the 16S rRNA genes revealed that strains B7-4 and B8-2 belonged to the same species (99.9% homology) and were most closely related to the aerobic alkaliphilic bacteriochlorophyll a-containing anoxygenic phototrophic bacterium (APB) Roseibacula alcaliphilum De (95.2%) and to NPB strains Rhodobaca barguzinensis VKM B-2406(T) (94.2%) and Rbc. bogoriensis LBB1(T) (93.9%). The isolates were closely related to the NPB Rhodobacter veldkampii DSM 11550(T) (94.8%) and to aerobic bacteriochlorophyll a-containing bacteria Roseinatronobacter monicus ROS 35(T) and Roseicitreum antarcticul ZS2-28(T) (93.5 and 93.9%, respectively). New strains were described as a new NPB genus and species of the family Rhodobacteriaceae, Rhodobaculum claviforme gen. nov., sp. nov., with B7-4(T) (VKM B-2708, LMG 28126) as the type strain.

Bacterial community under the hydrothermal system on the Suiyo Seamount: A model for archean and exo-biota

NASA Astrophysics Data System (ADS)

Yamagishi, A.

Microbial community in hydrothermal area at seafloor has been analyzed by culture-independent methods. Hydrothermal fluid from natural vents and vent chimneys have been analyzed by PCR (1-2). Hyperthermophilic microbes have been isolated from these environments (3-4). Though the analysis of these samples can provide the window to penetrate the microbial community under the seafloor, more direct analysis is desired for better understanding of the sub-seafloor microbial community In the ``Archaean Park Project'' supported by Special Coordination Fund, several holes were drilled and the holes were supported by casing pipes in the crater of the Suiyo seamount on the Izu-Bonin arc, West Pacific Ocean (about 1,400 m depth) in 2001 and 2002. Hydrothermal fluids were sampled from cased holes. The fluids were filtered to collect the microbial cells. The DNA was extracted and used to amplify 16S rDNA fragments by PCR (polymerase chain reaction) using a bacteria and an archaea specific primer sets. The PCR fragments were cloned and sequenced. FISH analysis revealed from 6 x103 to 2.5 x 106 bactrerial cells/ml in these hydrothermal fluids. PCR clone-analysis showed significant variation in bacterial sequences found in these samples. The species-patterns suggest that the contamination of ambient seawater to hydrothermal fluid samples is negligible. Difference in the dominant species depending on the location was found, suggesting that the bacterial community at sub-sea floor is not monotonous but has gradual shift from the hydrothermal center to peripheral area. The results suggest that there is chemo-autotrophic microbe-dependent biota under the hydrothermal system. References 1) Takai et al. Genetics 152: 1285-1297 (1999) 2) Takai et al. Appl. Environ. Microbioi. 67: 3618-3629 (2001) 3) Summit et al. Proc. Natl. Acad. Sci. 98: 2158-2163 (2001) 4) Amend, J. P. and Shodk, E. L. FEMS Microbiol. Rev. 25: 175-243 (2002)

Microbial diversity and iron oxidation at Okuoku-hachikurou Onsen, a Japanese hot spring analog of Precambrian iron formations.

PubMed

Ward, L M; Idei, A; Terajima, S; Kakegawa, T; Fischer, W W; McGlynn, S E

2017-11-01

Banded iron formations (BIFs) are rock deposits common in the Archean and Paleoproterozoic (and regionally Neoproterozoic) sedimentary successions. Multiple hypotheses for their deposition exist, principally invoking the precipitation of iron via the metabolic activities of oxygenic, photoferrotrophic, and/or aerobic iron-oxidizing bacteria. Some isolated environments support chemistry and mineralogy analogous to processes involved in BIF deposition, and their study can aid in untangling the factors that lead to iron precipitation. One such process analog system occurs at Okuoku-hachikurou (OHK) Onsen in Akita Prefecture, Japan. OHK is an iron- and CO 2 -rich, circumneutral hot spring that produces a range of precipitated mineral textures containing fine laminae of aragonite and iron oxides that resemble BIF fabrics. Here, we have performed 16S rRNA gene amplicon sequencing of microbial communities across the range of microenvironments in OHK to describe the microbial diversity present and to gain insight into the cycling of iron, oxygen, and carbon in this ecosystem. These analyses suggest that productivity at OHK is based on aerobic iron-oxidizing Gallionellaceae. In contrast to other BIF analog sites, Cyanobacteria, anoxygenic phototrophs, and iron-reducing micro-organisms are present at only low abundances. These observations support a hypothesis where low growth yields and the high stoichiometry of iron oxidized per carbon fixed by aerobic iron-oxidizing chemoautotrophs like Gallionellaceae result in accumulation of iron oxide phases without stoichiometric buildup of organic matter. This system supports little dissimilatory iron reduction, further setting OHK apart from other process analog sites where iron oxidation is primarily driven by phototrophic organisms. This positions OHK as a study area where the controls on primary productivity in iron-rich environments can be further elucidated. When compared with geological data, the metabolisms and mineralogy at OHK are most similar to specific BIF occurrences deposited after the Great Oxygenation Event, and generally discordant with those that accumulated before it. © 2017 John Wiley & Sons Ltd.

Spatial Differences in East Scotia Ridge Hydrothermal Vent Food Webs: Influences of Chemistry, Microbiology and Predation on Trophodynamics

PubMed Central

Reid, William D. K.; Sweeting, Christopher J.; Wigham, Ben D.; Zwirglmaier, Katrin; Hawkes, Jeffrey A.; McGill, Rona A. R.; Linse, Katrin; Polunin, Nicholas V. C.

2013-01-01

The hydrothermal vents on the East Scotia Ridge are the first to be explored in the Antarctic and are dominated by large peltospiroid gastropods, stalked barnacles (Vulcanolepas sp.) and anomuran crabs (Kiwa sp.) but their food webs are unknown. Vent fluid and macroconsumer samples were collected at three vent sites (E2, E9N and E9S) at distances of tens of metres to hundreds of kilometres apart with contrasting vent fluid chemistries to describe trophic interactions and identify potential carbon fixation pathways using stable isotopes. δ13C of dissolved inorganic carbon from vent fluids ranged from −4.6‰ to 0.8‰ at E2 and from −4.4‰ to 1.5‰ at E9. The lowest macroconsumer δ13C was observed in peltospiroid gastropods (−30.0‰ to −31.1‰) and indicated carbon fixation via the Calvin-Benson-Bassham (CBB) cycle by endosymbiotic gamma-Proteobacteria. Highest δ13C occurred in Kiwa sp. (−19.0‰ to −10.5‰), similar to that of the epibionts sampled from their ventral setae. Kiwa sp. δ13C differed among sites, which were attributed to spatial differences in the epibiont community and the relative contribution of carbon fixed via the reductive tricarboxylic acid (rTCA) and CBB cycles assimilated by Kiwa sp. Site differences in carbon fixation pathways were traced into higher trophic levels e.g. a stichasterid asteroid that predates on Kiwa sp. Sponges and anemones at the periphery of E2 assimilated a proportion of epipelagic photosynthetic primary production but this was not observed at E9N. Differences in the δ13C and δ34S values of vent macroconsumers between E2 and E9 sites suggest the relative contributions of photosynthetic and chemoautotrophic carbon fixation (rTCA v CBB) entering the hydrothermal vent food webs vary between the sites. PMID:23762393

Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation.

PubMed

Simmons, Sheri L; Dibartolo, Genevieve; Denef, Vincent J; Goltsman, Daniela S Aliaga; Thelen, Michael P; Banfield, Jillian F

2008-07-22

Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth approximately 20x). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types ( approximately 94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination.

Chemical and isotopic signature of bulk organic matter and hydrocarbon biomarkers within mid-slope accretionary sediments of the northern Cascadia margin gas hydrate system

USGS Publications Warehouse

Kaneko, Masanori; Shingai, Hiroshi; Pohlman, John W.; Naraoka, Hiroshi

2010-01-01

The chemical and isotopic compositions of sedimentary organic matter (SOM) from two mid-slope sites of the northern Cascadia margin were investigated during Integrated Ocean Drilling Program (IODP) Expedition 311 to elucidate the organic matter origins and identify potential microbial contributions to SOM. Gas hydrate is present at both locations (IODP Sites U1327 and U1328), with distinct patterns of near-seafloor structural accumulations at the cold seep Site U1328 and deeper stratigraphic accumulations at the slope-basin Site U1327. Source characterization and evidence that some components of the organic matter have been diagenetically altered are determined from the concentrations and isotopic compositions of hydrocarbon biomarkers, total organic carbon (TOC), total nitrogen (TN) and total sulfur (TS). The carbon isotopic compositions of TOC (δ13CTOC = −26 to −22‰) and long-chain n-alkanes (C27, C29 and C31, δ13C = −34 to − 29‰) suggest the organic matter at both sites is a mixture of 1) terrestrial plants that employ the C3 photosynthetic pathway and 2) marine algae. In contrast, the δ15NTN values of the bulk sediment (+ 4 to + 8‰) are consistent with a predominantly marine source, but these values most likely have been modified during microbial organic matter degradation. The δ13C values of archaeal biomarker pentamethylicosane (PMI) (− 46.4‰) and bacterial-sourced hopenes, diploptene and hop-21-ene (− 40.9 to − 34.7‰) indicate a partial contribution from methane carbon or a chemoautotrophic pathway. Our multi-isotope and biomarker-based conclusions are consistent with previous studies, based only on the elemental composition of bulk sediments, that suggested a mixed marine-terrestrial organic matter origin for these mid-slope sites of the northern Cascadia margin.

Trophic ecology and vertical patterns of carbon and nitrogen stable isotopes in zooplankton from oxygen minimum zone regions

NASA Astrophysics Data System (ADS)

Williams, Rebecca L.; Wakeham, Stuart; McKinney, Rick; Wishner, Karen F.

2014-08-01

The unique physical and biogeochemical characteristics of oxygen minimum zones (OMZs) influence plankton ecology, including zooplankton trophic webs. Using carbon and nitrogen stable isotopes, this study examined zooplankton trophic webs in the Eastern Tropical North Pacific (ETNP) OMZ. δ13C values were used to indicate zooplankton food sources, and δ15N values were used to indicate zooplankton trophic position and nitrogen cycle pathways. Vertically stratified MOCNESS net tows collected zooplankton from 0 to 1000 m at two stations along a north-south transect in the ETNP during 2007 and 2008, the Tehuantepec Bowl and the Costa Rica Dome. Zooplankton samples were separated into four size fractions for stable isotope analyses. Particulate organic matter (POM), assumed to represent a primary food source for zooplankton, was collected with McLane large volume in situ pumps. The isotopic composition and trophic ecology of the ETNP zooplankton community had distinct spatial and vertical patterns influenced by OMZ structure. The most pronounced vertical isotope gradients occurred near the upper and lower OMZ oxyclines. Material with lower δ13C values was apparently produced in the upper oxycline, possibly by chemoautotrophic microbes, and was subsequently consumed by zooplankton. Between-station differences in δ15N values suggested that different nitrogen cycle processes were dominant at the two locations, which influenced the isotopic characteristics of the zooplankton community. A strong depth gradient in zooplankton δ15N values in the lower oxycline suggested an increase in trophic cycling just below the core of the OMZ. Shallow POM (0-110 m) was likely the most important food source for mixed layer, upper oxycline, and OMZ core zooplankton, while deep POM was an important food source for most lower oxycline zooplankton (except for samples dominated by the seasonally migrating copepod Eucalanus inermis). There was no consistent isotopic progression among the four zooplankton size classes for these bulk mixed assemblage samples, implying overlapping trophic webs within the total size range considered.

Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation

PubMed Central

Denef, Vincent J; Goltsman, Daniela S. Aliaga; Thelen, Michael P; Banfield, Jillian F

2008-01-01

Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth ∼20×). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types (∼94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination. PMID:18651792

Drilling effect on subsurface microbial community structure in groundwater from the -250 m gallery at the Horonobe Underground Research Laboratory, Japan

NASA Astrophysics Data System (ADS)

Ise, K.; Amano, Y.; Sasaki, Y.; Yoshikawa, H.

2014-12-01

The deep geological disposal system is regarded as the most secure and practical disposal method of high-level radioactive waste in the world. In this disposal system, preservation of reducing condition is one of the key requirements, because most of radionuclides have low solubilities in such condition. However, the host rocks near the shafts and galleries would be affected by oxidization during the construction and operation period of a repository (for about 50 years). Therefore, the recovery of reducing condition after closing the repository should be verified. During the recovery processes, it is considered that microbial activities play important roles, but the mechanisms are poorly understood. In this study, we monitored the changes in microbial communities by molecular method to evaluate microbial response toward the oxygen stress. The groundwater samples were collected from a borehole of 250 m depth at the Horonobe Underground Research Laboratory, for two years immediately after drilling of a borehole without any contamination as much as possible. Immediately after drilling of the borehole, the phylotype related to Arcobacter spp. was dominated about 65 % of the total clone library. Arcobacter spp. is known as sulfide oxidizer and which can growth chemoautotrophically. Half a year later, the phylotype related to Azoarcus spp. and Pseudomonas spp. known as nitrate reducing bacteria increased, instead of the phylotype related to Arcobacter spp. One year later, in addition to nitrate reducing bacteria, phylotype related to Dethiobacterspp. known as thiosulfate reducing bacteria was dominantly detected. Two years later, most of detected clones were related to uncultured species such as candidate division WS6 and JS1 which are detected frequently in deep-sea sediments. Our results indicate that these redox sequential reactions could contribute to the recovery and maintenance of reducing conditions and provide a conceptual model for evaluating the capacity to recover reducing conditions in subsurface environments after final geological disposal and the post-closure.

High resolution shallow imaging of the mega-splay fault in the central Nankai Trough off Kumano

NASA Astrophysics Data System (ADS)

Ashi, J.

2012-12-01

Steep slopes are continuously developed at water depths between 2200 to 2800 m at the Nankai accretionary prism off Kumano. These slopes are interpreted to be surface expressions caused by the megasplay fault on seismic reflection profiles. The fault plane has been drilled at multiple depths below seafloor by IODP NanTroSEIZE project. Mud breccias only recognized at the hanging wall of the fault (Site C0004) by Xray CT scanner are interpreted be formed by strong ground shaking and the age of the shallowest event of mud breccia layers suggests deformation in 1944 Tonankai earthquake (Sakaguchi et al., 2011). Detailed structures around the fault have been examined by seismic reflection profiles including 3D experiments. Although the fault plane deeper than 100 m is well imaged, the structure shallower than 100 m is characterized by obscure sediment veneer suggesting no recent fault activity. Investigation of shallow deformation structures is significant for understanding of recent tectonic activity. Therefore, we carried out deep towed subbottom profile survey by ROV NSS (Navigable Sampling System) during Hakuho-maru KH-11-9 cruise. We introduced a chirp subbottom profiling system of EdgeTech DW-106 for high resolution mapping of shallow structures. ROV NSS also has capability to take a long core with a pinpoint accuracy. The subbottom profiler crossing the megasplay fault near Site C0004 exhibits a landward dipping reflector suggesting the fault plane. The shallowest depth of the reflector is about 10 m below seafloor and the strata above it shows reflectors parallel to the seafloor without any topographic undulation. The fault must have displaced the shallow formation because intense deformation indicated by mud breccia was restricted to near fault zone. Slumping or sliding probably modified the shallow formation after the faulting. The shallow deformations near the megasplay fault were well imaged at the fault scarp 20 km southwest of Site C0004. Although the fault plane itself is not recognized, displacements of sedimentary layers are observed along the fault up to 30 meter below the seafloor. Landward dip of the fault is estimated to be 30 degrees. Displacements of strata are about 3 m near the surface and about 5 m at 7 m below the seafloor suggesting accumulation of fault displacement. The structure more than 30 m below the seafloor is obscure due to decrease of acoustic signal. Active cold seep is expected in this site by high heat flow (Yamano et al., 2012) and many trails of Calyptogena detected by seafloor observations. These results are consistent with the shallow structures reveled by our subbottom profiling survey. References Sakaguchi, A. et al., Geology 39, 919-922, 2011. Yamano, M. et al., JpGU Meeting abstract, SSS38-P23, 2012

Landscape-scale effects of fire severity on mixed-conifer and red fir forest structure in Yosemite National Park

USGS Publications Warehouse

Kane, Van R.; Lutz, James A.; Roberts, Susan L.; Smith, Douglas F.; McGaughey, Robert J.; Povak, Nicholas A.; Brooks, Matthew L.

2013-01-01

While fire shapes the structure of forests and acts as a keystone process, the details of how fire modifies forest structure have been difficult to evaluate because of the complexity of interactions between fires and forests. We studied this relationship across 69.2 km2 of Yosemite National Park, USA, that was subject to 32 fires ⩾40 ha between 1984 and 2010. Forests types included ponderosa pine (Pinus ponderosa), white fir-sugar pine (Abies concolor/Pinus lambertiana), and red fir (Abies magnifica). We estimated and stratified burned area by fire severity using the Landsat-derived Relativized differenced Normalized Burn Ratio (RdNBR). Airborne LiDAR data, acquired in July 2010, measured the vertical and horizontal structure of canopy material and landscape patterning of canopy patches and gaps. Increasing fire severity changed structure at the scale of fire severity patches, the arrangement of canopy patches and gaps within fire severity patches, and vertically within tree clumps. Each forest type showed an individual trajectory of structural change with increasing fire severity. As a result, the relationship between estimates of fire severity such as RdNBR and actual changes appears to vary among forest types. We found three arrangements of canopy patches and gaps associated with different fire severities: canopy-gap arrangements in which gaps were enclosed in otherwise continuous canopy (typically unburned and low fire severities); patch-gap arrangements in which tree clumps and gaps alternated and neither dominated (typically moderate fire severity); and open-patch arrangements in which trees were scattered across open areas (typically high fire severity). Compared to stands outside fire perimeters, increasing fire severity generally resulted first in loss of canopy cover in lower height strata and increased number and size of gaps, then in loss of canopy cover in higher height strata, and eventually the transition to open areas with few or no trees. However, the estimated fire severities at which these transitions occurred differed for each forest type. Our work suggests that low severity fire in red fir forests and moderate severity fire in ponderosa pine and white fir-sugar pine forests would restore vertical and horizontal canopy structures believed to have been common prior to the start of widespread fire suppression in the early 1900s. The fusion of LiDAR and Landsat data identified post-fire structural conditions that would not be identified by Landsat alone, suggesting a broad applicability of combining Landsat and LiDAR data for landscape-scale structural analysis for fire management.

Relative Importance of Chemoautotrophy for Primary Production in a Light Exposed Marine Shallow Hydrothermal System.

PubMed

Gomez-Saez, Gonzalo V; Pop Ristova, Petra; Sievert, Stefan M; Elvert, Marcus; Hinrichs, Kai-Uwe; Bühring, Solveig I

2017-01-01

The unique geochemistry of marine shallow-water hydrothermal systems promotes the establishment of diverse microbial communities with a range of metabolic pathways. In contrast to deep-sea vents, shallow-water vents not only support chemosynthesis, but also phototrophic primary production due to the availability of light. However, comprehensive studies targeting the predominant biogeochemical processes are rare, and consequently a holistic understanding of the functioning of these ecosystems is currently lacking. To this end, we combined stable isotope probing of lipid biomarkers with an analysis of the bacterial communities to investigate if chemoautotrophy, in parallel to photoautotrophy, plays an important role in autotrophic carbon fixation and to identify the key players. The study was carried out at a marine shallow-water hydrothermal system located at 5 m water depth off Dominica Island (Lesser Antilles), characterized by up to 55°C warm hydrothermal fluids that contain high amounts of dissolved Fe 2+ . Analysis of the bacterial diversity revealed Anaerolineae of the Chloroflexi as the most abundant bacterial class. Furthermore, the presence of key players involved in iron cycling generally known from deep-sea hydrothermal vents (e.g., Zetaproteobacteria and Geothermobacter ), supported the importance of iron-driven redox processes in this hydrothermal system. Uptake of 13 C-bicarbonate into bacterial fatty acids under light and dark conditions revealed active photo- and chemoautotrophic communities, with chemoautotrophy accounting for up to 65% of the observed autotrophic carbon fixation. Relatively increased 13 C-incorporation in the dark allowed the classification of ai C 15:0 , C 15:0 , and i C 16:0 as potential lipid biomarkers for bacterial chemoautotrophy in this ecosystem. Highest total 13 C-incorporation into fatty acids took place at the sediment surface, but chemosynthesis was found to be active down to 8 cm sediment depth. In conclusion, this study highlights the relative importance of chemoautotrophy compared to photoautotrophy in a shallow-water hydrothermal system, emphasizing chemosynthesis as a prominent process for biomass production in marine coastal environments influenced by hydrothermalism.

Aseptically Sampled Organics in Subsurface Rocks From the Mars Analog Rio Tinto Experiment: An Analog For The Search for Deep Subsurface Life on Mars.}

NASA Astrophysics Data System (ADS)

Bonaccorsi, R.; Stoker, C. R.

2005-12-01

The subsurface is the key environment for searching for life on planets lacking surface life. Subsurface ecosystems are of great relevance to astrobiology including the search for past/present life on Mars. The surface of Mars has conditions preventing current life but the subsurface might preserve organics and even host some life [1]. The Mars-Analog-Rio-Tinto-Experiment (MARTE) is performing a simulation of a Mars drilling experiment. This comprises conventional and robotic drilling of cores in a volcanically-hosted-massive-pyrite deposit [2] from the Iberian Pyritic Belt (IBP) and life detection experiments applying anti-contamination protocols (e.g., ATP Luminometry assay). The RT is considered an important analog of the Sinus Meridiani site on Mars and an ideal model analog for a deep subsurface Martian environment. Former results from MARTE suggest the existence of a relatively complex subsurface life including aerobic and anaerobic chemoautotrophs and strict anaerobic methanogens sustained by Fe and S minerals in anoxic conditions. A key requirement for the analysis of a subsurface sample on Mars is a set of simple tests that can help determine if the sample contains organic material of biological origin, and its potential for retaining definitive biosignatures. We report here on the presence of bulk organic matter Corg (0.03-0.05 Wt%), and Ntot (0.01-0.04 Wt%) and amount of measured ATP (Lightning MVP, Biocontrol) in weathered rocks (tuffs, gossan, pyrite stockwork from Borehole #8; >166m). This provides key insight on the type of trophic system sustaining the subsurface biosphere (i.e., heterotrophs vs. autotrophs) at RT. ATP data (Relative-Luminosity-Units, RLU) provide information on possible contamination and distribution of viable biomass with core depth (BH#8, and BH#7, ~3m). Avg. 153 RLU, i.e., surface vs. center of core, suggest that cleaness/sterility can be maintained when using a simple sterile protocol under field conditions. Results from this research will support future drilling mission planned on Mars. [1] Boston, P.J., et al., 1992. Icarus 95,300-308; [2] Leistel et al., 1998.

Metagenomic Assembly of the Dominant Zetaproteobacteria in an Iron-oxidizing Hydrothermal Microbial Mat

NASA Astrophysics Data System (ADS)

Moyer, C. L.; Fullerton, H.

2013-12-01

Iron is the fourth most abundant element in the Earth's crust and is potentially one of the most abundant energy sources on the earth as an electron donor for chemolithoautotrophic growth coupled to Fe(II) oxidation. Despite the rapid abiotic oxidation rate of iron, many microbes have adapted to feeding off this fleeting energy source. One such bacterial class is the Zetaproteobacteria. Iron-dominated microbial mat material was collected with a small-scale syringe sampler from Loihi Seamount, Hawaii. From this sample, gDNA was extracted and prepared for paired-end Illumina sequencing. Reconstruction of SSU rDNA genes using EMERGE allowed for comparison to previous SSU rDNA surveys. Clone libraries and qPCR show these microbial mats to be dominated by Zetaproteobacteria. Results from our in silico reconstruction confirm these initial findings. RDP classification of the EMERGE reconstructed sequences resulted in 44% of the community being identified as Zetaproteobacteria. The most abundant SSU rDNA has 99% similarity to Zeta OTU-2, and only a 94% similarity to M. ferrooxidans PV-1. Zeta OTU-2 has been shown to be the most cosmopolitan population in iron-dominated hydrothermal systems from across Pacific Ocean. Metagenomic assembly has resulted in many contigs with high identity to M. ferrooxidans as identified, by BLAST. However, with large differences in SSU rRNA similarity, M. ferrooxidans PV-1 is not an adequate reference. Current work is focusing on reconstruction of the dominant microbial mat member, without the use of a reference genome through an iterative assembly approach. The resulting 'pan-genome' will be compared to other Zetaproteobacteria (at the class level) and the functional ecology of this cosmopolitan microbial mat community member will be extrapolated. Thus far, we have detected multiple housekeeping genes involved in DNA replication, transcription and translation. The most abundant metabolic gene we have found is Aconitase, a key enzyme in the TCA cycle. The presence of Molybdopterin oxidoreductase, ferric uptake regulation protein, cytochromes, thioredoxin, RuBisCo and other TCA related genes support our hypothesis of chemoautotrophic primary production with the notion that Zetaproteobacteria act as ecosystem engineers driving microbial mat formation and maintenance of their habitat.

The Precambrian Biogeochemical Carbon Isotopic Record: Contributions of Thermal Versus Biological Processes

NASA Technical Reports Server (NTRS)

DesMarais, David J.; DeVincenzi, Donald L. (Technical Monitor)

2000-01-01

Superplumes offer a new approach for understanding global C cycles. Isotopes help to discern the impacts of geological, environmental and biological processes ujpun the evolution of these cycles. For example, C-13/C-12 values of coeval sedimentary organics and carbonates give global estimates of the fraction of C buried as organics (Forg), which today lies near 0.2. Before Oxygenic photosynthesis arose, our biosphere obtained reducing power for biosynthesis solely from thermal volatiles and rock alteration. Thus Forg was dominated by the mantle redox state, which has remained remarkably constant for greater than Gy. Recent data confirm that the long-term change in Forg had been small, indicating that the mantle redox buffer remains important even today. Oxygenic photosynthesis enabled life to obtain additional reducing power by splitting the water molecule. Accordingly, biological organic production rose above the level constrained by the mantle-derived flux of reduced species. For example, today, chemoautotrophs harvesting energy from hydrothermal emanations can synthesize at most between 0.2 x 10(exp 12) and 2x 10(exp 12) mol C yr-1 of organic C globally. In contrast, global photosynthetic productivity is estimated at 9000 x 10(exp 12) mol C yr-1. Occasionally photosynthetic productivity did contribute to dramatically -elevated Forg values (to 0.4 or more) as evidenced by very high carbonate C-13/C-12. The interplay between biological, tectonic and other environmental factors is illustrated by the mid-Archean to mid-Proterozoic isotopic record. The relatively constant C-13/C-12 values of Archean carbonates support the view that photosynthetically-driven Forg increases were not yet possible. In contrast, major excursions in C-13/C-12, and thus also in Forg, during the early Proterozoic confirmed the global importance of oxygenic photosynthesis by that time. Remarkably, the superplume event at 1.9 Ga did not trigger another major Forg increase, despite the favorable conditions for organic burial that were evidenced by elevated sea levels and higher black shale abundances. Perhaps those superplume-rated processes that favored enhanced organic burial were offset by the ability of mantle-derived redox buffering, which was enhanced during the superplume event, to limit excursions in Forg.

Sources of organic carbon for Rimicaris hybisae: Tracing individual fatty acids at two hydrothermal vent fields in the Mid-Cayman rise

NASA Astrophysics Data System (ADS)

Streit, Kathrin; Bennett, Sarah A.; Van Dover, Cindy L.; Coleman, Max

2015-06-01

Hydrothermal vents harbor ecosystems mostly decoupled from organic carbon synthesized with the energy of sunlight (photosynthetic carbon source) but fueled instead by oxidation of reduced compounds to generate a chemosynthetic carbon source. Our study aimed to disentangle photosynthetic and chemosynthetic organic carbon sources for the shrimp species Rimicaris hybisae, a primary consumer presumed to obtain its organic carbon mainly from ectosymbiotic chemoautotrophic bacteria living on its gill cover membrane. To provide ectosymbionts with ideal conditions for chemosynthesis, these shrimp live in dense clusters around vent chimneys; they are, however, also found sparsely distributed adjacent to diffuse vent flows, where they might depend on alternative food sources. Densely and sparsely distributed shrimp were sampled and dissected into abdominal tissue and gill cover membrane, covered with ectosymbiotic bacteria, at two hydrothermal vent fields in the Mid-Cayman rise that differ in vent chemistry. Fatty acids (FA) were extracted from shrimp tissues and their carbon isotopic compositions assessed. The FA data indicate that adult R. hybisae predominantly rely on bacteria for their organic carbon needs. Their FA composition is dominated by common bacterial FA of the n7 family (~41%). Bacterial FA of the n4 FA family are also abundant and found to constitute good biomarkers for gill ectosymbionts. Sparsely distributed shrimp contain fractions of n4 FA in gill cover membranes ~4% lower than densely packed ones (~18%) and much higher fractions of photosynthetic FA in abdominal tissues, ~4% more (compared with 1.6%), suggesting replacement of ectosymbionts along with exoskeletons (molt), while they take up alternative diets of partly photosynthetic organic carbon. Abdominal tissues also contain photosynthetic FA from a second source taken up presumably during an early dispersal phase and still present to c. 3% in adult shrimp. The contribution of photosynthetic carbon to the FA pool of adult R. hybisae is, however, overall small (max. 8%). Significant differences in carbon isotopic values of chemosynthetically derived FA between vent fields suggest that different dominant C fixation pathways are being used.

The origin of decoupled carbonate and organic carbon isotope signatures in the early Cambrian (ca. 542-520 Ma) Yangtze platform

NASA Astrophysics Data System (ADS)

Jiang, Ganqing; Wang, Xinqiang; Shi, Xiaoying; Xiao, Shuhai; Zhang, Shihong; Dong, Jin

2012-02-01

The early Cambrian (ca. 542-520 Ma) strata in South China record two prominent negative carbonate carbon isotope (δ13Ccarb) excursions of early Nemakit-Daldynian (N-D) and early Tommotian ages. Across each of these excursions, carbonate and organic carbon isotopes (δ13Ccarb and δ13Corg) are strongly decoupled. Regional correlation across a shelf-to-basin transect shows lateral heterogeneity of δ13Corg during the early-middle N-D but more homogenized δ13Corg values across the basin during the late N-D and Tommotian. The temporal and lateral variations in δ13Corg suggest that decoupled δ13Ccarb and δ13Corg across the N-D δ13Ccarb excursion were possibly caused by diagenetic alteration of organic matter and/or amplification of detrital organic carbon isotope signature in low-TOC carbonates. In contrast, decoupled δ13Ccarb and δ13Corg of the upper N-D and Tommotian were likely resulted from chemoautotrophic-methanotrophic biomass contribution to TOC in organic-rich black shale and carbonates. The decoupled δ13Ccarb-δ13Corg pattern from the lower N-D strata (ca. 542 Ma) shows striking similarities with those from the basal (ca. 635 Ma) and upper (ca. 551 Ma) Doushantuo Formation. In all three cases, decoupled δ13Ccarb-δ13Corg are seen in organic-poor carbonates (TOC ≤ 0.1‰) and coupled δ13Ccarb-δ13Corg occur in organic-rich black shale and carbonates at the end of the negative δ13Ccarb excursion. These similarities suggest that the shift from decoupled to coupled δ13Ccarb-δ13Corg has no causal link with the terminal oxidation of a large oceanic DOC reservoir. Given the pervasive anoxia/euxinia in Ediacaran-early Cambrian oceans, local DOC-rich environments may have been common, but a large oceanic DOC reservoir capable of buffering the δ13C of marine organic matter requires independent evidence.

Microbially mediated carbon cycling as a control on the δ 13C of sedimentary carbon in eutrophic Lake Mendota (USA): new models for interpreting isotopic excursions in the sedimentary record

NASA Astrophysics Data System (ADS)

Hollander, David J.; Smith, Michael A.

2001-12-01

An isotopic study of various carbon phases in eutrophic Lake Mendota (Wisconsin, USA) indicates that the δ13C composition of sedimentary organic and inorganic carbon has become more negative in response to increasing microbially mediated carbon cycling and processes associated with the intensification of seasonal and long-term eutrophication. Progressive increases in the contributions of isotopically depleted chemoautotrophic and methanotrophic biomass (reflected in the -40 to -90‰ values of hopanols and FAMES), attributed to seasonal and long-term increases in production and expansion of the anaerobic water mass, accounts for carbon isotopic trends towards depleted δ13C values observed in both seasonal varves and over the past 100 years. Changes in the intensities of certain microbial processes are also evident in the sedimentary geochemical record. During the period of most intense cultural eutrophication, when the oxic-anoxic interface was located close to the surface, methanogenesis/methanotrophy and the oxidation of biogenic methane increased to the extent that significant quantities of 13C-depleted CO2 were added into the epilimnion. This depleted CO2 was subsequently utilized by phytoplankton and incorporated into CaCO3 during biogenically induced calcite precipitation. A comparative study between eutrophic Lakes Mendota and Greifen, further indicate that the extent of nutrient loading in the epilimnion determines whether the δ13C record of sedimentary organic carbon reflects intensification of microbial processes in the hypolimnion and sediments, or changes in the primary productivity in the photic zone. From this comparison, a series of eutrophication models are developed to describe progressive transitions through thresholds of microbial and eukaryotic productivity and their influence on the δ13C record of sedimentary carbon. With increasing eutrophication, the models initially predict a negative and then a subsequent positive carbon isotopic excursion reflecting the changing influence of 13C-deleted microbial biomass relative to 13C-enriched photoautrophic biomass. These eutrophication models provide a framework to evaluate carbon cycling processes in modern environments and have significant implications for interpreting carbon isotopic excursions in the sedimentary record.

Assessing the Potential for Ancient Habitable Environments in Gusev Crater, Mars

NASA Astrophysics Data System (ADS)

Des Marais, D. J.; Athena Science Team

2007-12-01

In order to be habitable for microbial life as we know it, an environment must provide nutrient elements, energy and liquid water. We assess the potential for habitable environments in the areas explored by the MER rover Spirit. These areas include the basaltic plains near Columbia Memorial Station, West Spur, Husband Hill, and the inner basin south of Husband Hill. Little aqueous activity apparently occurred in Gusev crater since the basaltic plains were emplaced in Hesperian times, therefore the basaltic plains were highly unlikely to have sustained habitable environments. The Columbia Hills, located ~3 km southeast of the landing site, are older than the surrounding basaltic plains. Aqueous processes have extensively altered bedrock in the Columbia Hills. Ferrous iron in the original, unaltered parent rock of hills materials has typically been oxidized extensively to form ferric oxides, hydroxides, and other ferric minerals. Migrating fluids have removed Ca and other cations, allowing residual Al to become relatively more abundant, and fluids added sulfates and chlorides. In subsurface environments on Earth, microorganisms can obtain key nutrients from the weathering of basalts. Materials examined in the Columbia Hills have comparable or greater abundances of these elements than do MORB. Wishstone rock and Watchtower outcrop have very high contents of phosphorous. Chemoautotrophs ("chemical- feeders" that obtain energy from inorganic chemicals) can thrive in subsurface environments. Mixing oxidized constituents from surface environments with generally more reduced constituents from subsurface rocks and thermal emanations provides energy to sustain microorganisms. Ferrous iron in parent materials in the Columbia Hills has been oxidized to form a variety of ferric minerals. On Earth, microbial processes have been documented to contribute to the production of goethite, hematite and other iron oxides. Observations by Spirit are consistent with the possibility that liquid water, nutrients and sources of chemical energy were simultaneously available to sustain habitable conditions in subsurface Columbia Hills materials at least some time in the distant (Noachian?) past. There is as yet no evidence that these conditions ever existed at the surface. Future research must seek to determine whether ancient migrating fluids in Gusev ever achieved the water activity necessary to sustain life.

Influence of seep emission on the non-symbiont-bearing fauna and vagrant species at an active giant pockmark in the Gulf of Guinea (Congo-Angola margin)

NASA Astrophysics Data System (ADS)

Olu, K.; Caprais, J. C.; Galéron, J.; Causse, R.; von Cosel, R.; Budzinski, H.; Ménach, K. Le; Roux, C. Le; Levaché, D.; Khripounoff, A.; Sibuet, M.

2009-12-01

Detailed surveying with an ROV found that a dense and diverse cold-seep community colonises a giant pockmark located at 3200 m depth, 8 km north from the deep Congo channel. Several types of assemblages, either dominated by Mytilidae and Vesicomyidae bivalves or Siboglinidae polychaetes, are distributed on the 800-m diameter active area. The site is characterised by a most active central zone in a depression with abundant carbonate concretions and high methane fluxes where high-density clusters of mussels and siboglinids dominate. In contrast, the peripheral zones display large fields of dead and live vesicomyids on soft sediment, with a lower mean density and lower methane concentration in seawater. The associated megafauna includes Alvinocarididae shrimps, echinoids, holothurians of the family Synaptidae, several species of gastropods, two species of galatheids, and Zoarcidae and Ophidiidae fishes. Multivariate analyses of video transect data show that the distribution of these major megafauna species at the pockmark scale is influenced by the habitat heterogeneity due to fluid or gas emission, occurrence of hydrates, substratum variability and by the presence of large symbiont-bearing species. Several assemblages dominated either by mytilids, vesicomyids, or siboglinids have been sampled for megafauna densities and biomass estimations and stable isotope measurements ( δ13C and δ15N) of dominant species and food sources. The highest estimates of megafauna densities have been obtained in mytilid beds. According to their stable isotopes values, non-symbiont-bearing species mainly rely on chemosynthesis-originated carbon, either as primary consumers of chemoautotrophic microorganisms, or at higher trophic level recycling organic matter, or relying on bivalve and tubeworm production. Most of them likely feed on different sources like shrimps, but differences according to habitat have been evidenced. Carbon and nitrogen isotope ratios of galatheids and benthic or benthopelagic fishes captured by trawls at increasing distances from the pockmark provide evidence of the high variability in the proportion of chemosynthesis-originated carbon in their diet, from 15% to 38%, according to the species captured as far as 4 km to the site.

Geochemical Evidence for Recent Hydrothermal Alteration of Marine Sediments in Mid-Okinawa Trough, Southwest Japan

NASA Astrophysics Data System (ADS)

Tanaka, A.; Abe, G.; Yamaguchi, K. E.

2014-12-01

Recent studies have shown that submarine hydrothermal system supports diverse microbial life. Bio-essential metals supporting such microbial communities were released from basalts by high-temperature water-rock interaction in deeper part of the oceanic crust and carried by submarine fluid flow. Its total quantity in global hydrothermal settings has been estimated to be on the order of ~1019 g/yr, which is surprisingly on the same order of the total river flows (Urabe et al., 2011). Therefore, it is important to explore how submarine river system works, i.e., to understand mechanism and extent of elemental transport, which should lead to understanding of the roles of hydrothermal circulation in oceanic crust in controlling elemental budget in the global ocean and geochemical conditions to support deep hot biosphere. 　We performed REE analysis of marine sediments influenced by submarine hydrothermal activity in Mid-Okinawa Trough. The sediment samples used in this study are from IODP site at Iheya North region and JADE site at Izena region. The samples show alternation between volcanic and clastic sediments. Hydrothermal fluids of this area contain elevated concentrations of volatile components such as H2, CO2, CH4, NH4+, and H2S, supporting diverse chemoautotrophic microbial community (Nakagawa et al., 2005). The purpose of this study is to examine the effect of hydrothermal activity on the REE signature of the sediments. Chondrite-normalized REE patterns of the samples show relative enrichment of light over heavy REEs, weak positive Ce anomalies, and variable degrees of negative Eu anomalies. The REE patterns suggest the sediments source was mainly basalt, suggesting insignificant input of continental materials. Negative Eu anomalies found in the IODP site become more pronounced with increasing depth, suggesting progressive increase of hydrothermal alteration where Eu was reductively dissolved into fluids by decomposition of feldspars. Contrary, at the JADE site, magnitude of negative Eu anomalies was variable independent of the sediment depth. This suggests changes in the redox conditions, most likely due to occasional invasions of O2-bearing seawater into sediments. Different regimes of hydrothermal fluid flows govern the chemical environments of marine sediments in active hydrothermal areas.

Relative Importance of Chemoautotrophy for Primary Production in a Light Exposed Marine Shallow Hydrothermal System

PubMed Central

Gomez-Saez, Gonzalo V.; Pop Ristova, Petra; Sievert, Stefan M.; Elvert, Marcus; Hinrichs, Kai-Uwe; Bühring, Solveig I.

2017-01-01

The unique geochemistry of marine shallow-water hydrothermal systems promotes the establishment of diverse microbial communities with a range of metabolic pathways. In contrast to deep-sea vents, shallow-water vents not only support chemosynthesis, but also phototrophic primary production due to the availability of light. However, comprehensive studies targeting the predominant biogeochemical processes are rare, and consequently a holistic understanding of the functioning of these ecosystems is currently lacking. To this end, we combined stable isotope probing of lipid biomarkers with an analysis of the bacterial communities to investigate if chemoautotrophy, in parallel to photoautotrophy, plays an important role in autotrophic carbon fixation and to identify the key players. The study was carried out at a marine shallow-water hydrothermal system located at 5 m water depth off Dominica Island (Lesser Antilles), characterized by up to 55°C warm hydrothermal fluids that contain high amounts of dissolved Fe2+. Analysis of the bacterial diversity revealed Anaerolineae of the Chloroflexi as the most abundant bacterial class. Furthermore, the presence of key players involved in iron cycling generally known from deep-sea hydrothermal vents (e.g., Zetaproteobacteria and Geothermobacter), supported the importance of iron-driven redox processes in this hydrothermal system. Uptake of 13C-bicarbonate into bacterial fatty acids under light and dark conditions revealed active photo- and chemoautotrophic communities, with chemoautotrophy accounting for up to 65% of the observed autotrophic carbon fixation. Relatively increased 13C-incorporation in the dark allowed the classification of aiC15:0, C15:0, and iC16:0 as potential lipid biomarkers for bacterial chemoautotrophy in this ecosystem. Highest total 13C-incorporation into fatty acids took place at the sediment surface, but chemosynthesis was found to be active down to 8 cm sediment depth. In conclusion, this study highlights the relative importance of chemoautotrophy compared to photoautotrophy in a shallow-water hydrothermal system, emphasizing chemosynthesis as a prominent process for biomass production in marine coastal environments influenced by hydrothermalism. PMID:28484442

Hot spring microbial community composition, morphology, and carbon fixation: implications for interpreting the ancient rock record

NASA Astrophysics Data System (ADS)

Schuler, Caleb G.; Havig, Jeff R.; Hamilton, Trinity L.

2017-11-01

Microbial communities in hydrothermal systems exist in a range of macroscopic morphologies including stromatolites, mats, and filaments. The architects of these structures are typically autotrophic, serving as primary producers. Structures attributed to microbial life have been documented in the rock record dating back to the Archean including recent reports of microbially-related structures in terrestrial hot springs that date back as far as 3.5 Ga. Microbial structures exhibit a range of complexity from filaments to more complex mats and stromatolites and the complexity impacts preservation potential. As a result, interpretation of these structures in the rock record relies on isotopic signatures in combination with overall morphology and paleoenvironmental setting. However, the relationships between morphology, microbial community composition, and primary productivity remain poorly constrained. To begin to address this gap, we examined community composition and carbon fixation in filaments, mats, and stromatolites from the Greater Obsidian Pool Area (GOPA) of the Mud Volcano Area, Yellowstone National Park, WY. We targeted morphologies dominated by bacterial phototrophs located in close proximity within the same pool which are exposed to similar geochemistry as well as bacterial mat, algal filament and chemotrophic filaments from nearby springs. Our results indicate i) natural abundance δ13C values of biomass from these features (-11.0 to -24.3 ‰) are similar to those found in the rock record; ii) carbon uptake rates of photoautotrophic communities is greater than chemoautotrophic; iii) oxygenic photosynthesis, anoxygenic photosynthesis, and chemoautotrophy often contribute to carbon fixation within the same morphology; and iv) increasing phototrophic biofilm complexity corresponds to a significant decrease in rates of carbon fixation—filaments had the highest uptake rates whereas carbon fixation by stromatolites was significantly lower. Our data highlight important differences in primary productivity between structures despite indistinguishable δ13C values of the biomass. Furthermore, low primary productivity by stromatolites compared to other structures underscores the need to consider a larger role for microbial mats and filaments in carbon fixation and O2 generation during the Archean and Proterozoic.

Using metatranscriptomics to understand the roles of Fe(II)-oxidizing microbes in marine hydrothermal vents

NASA Astrophysics Data System (ADS)

Glazer, B. T.; Mcallister, S.; Polson, S. W.; Chan, C. S. Y.

2015-12-01

Fe(II)-oxidizing microbes (FeOM) are thought to be key players in marine Fe cycling, particularly at hydrothermal vents. However, we do not have tools to track their activity, largely because we do not know the genes involved in neutrophilic chemolithotrophic Fe oxidation. Researchers have used gene homology between FeOM isolates to suggest several genes that may be involved in Fe(II) oxidation, including the Fe oxidase cyc2 found in the Zetaproteobacteria type strain Mariprofundus ferrooxydans, as well as all other known neutrophilic microaerophilic FeOM. Although many Zetaproteobacteria are found within natural Fe mats, close relatives of Fe(II)-oxidizing isolates are rarely present. Therefore, one goal of this study was to determine the activity of putative Fe(II) oxidation genes in dominant OTUs found in natural environments. We collected Fe mats from hydrothermal vents at Loihi Seamount, Hawaii, preserving RNA in situ. By analyzing metatranscriptomes of different Fe mat niches, we were able to determine the OTUs involved and the gene expression patterns associated with Fe(II) oxidation in the marine environment. Analysis of metatranscriptomic data confirms that the Zetaproteobacteria express the various genes necessary to support the Fe mat community through chemoautotrophic growth. Globally ubiquitous and even some rare species of the Zetaproteobacteria were active, with different relative abundances depending on Fe mat niches defined by fluid flow and geochemistry. Initial results show that genes thought to be involved in the electron transport pathway from Fe(II) to O2, including cyc2, are some of the most highly expressed genes in marine Fe microbial mats. Species-specific variants of these genes suggest that many of the Zetaproteobacteria species, spanning the breadth of the diversity of the class, are expressing genes necessary for Fe(II) oxidation within natural Fe mat niches. Understanding the differential expression of these genes in different niches will enable us to quantify the activity of marine FeOM and their effect on Fe and associated element cycling within deep and coastal marine systems.

Enabling technologies to improve area-wide integrated pest management programmes for the control of screwworms.

PubMed

Robinson, A S; Vreysen, M J B; Hendrichs, J; Feldmann, U

2009-06-01

The economic devastation caused in the past by the New World screwworm fly Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae) to the livestock industry in the U.S.A., Mexico and the rest of Central America was staggering. The eradication of this major livestock pest from North and Central America using the sterile insect technique (SIT) as part of an area-wide integrated pest management (AW-IPM) programme was a phenomenal technical and managerial accomplishment with enormous economic implications. The area is maintained screwworm-free by the weekly release of 40 million sterile flies in the Darien Gap in Panama, which prevents migration from screwworm-infested areas in Columbia. However, the species is still a major pest in many areas of the Caribbean and South America and there is considerable interest in extending the eradication programme to these countries. Understanding New World screwworm fly populations in the Caribbean and South America, which represent a continuous threat to the screwworm-free areas of Central America and the U.S.A., is a prerequisite to any future eradication campaigns. The Old World screwworm fly Chrysomya bezziana Villeneuve (Diptera: Calliphoridae) has a very wide distribution ranging from Southern Africa to Papua New Guinea and, although its economic importance is assumed to be less than that of its New World counterpart, it is a serious pest in extensive livestock production and a constant threat to pest-free areas such as Australia. In the 1980s repeated introductions and an expansion of Old World screwworm populations were reported in the Middle East; in the 1990s it invaded Iraq and since late 2007 it has been reported in Yemen, where a severe outbreak of myiasis occurred in 2008. Small-scale field trials have shown the potential of integrating the SIT in the control of this pest and various international organizations are considering using the release of sterile insects as part of an AW-IPM approach on a much wider scale. Wohlfahrtia magnifica (Schiner) (Diptera: Sarcophagidae) is a screwworm of temperate regions, which, although of limited agricultural importance, has invaded several new locations in the past few years. This special issue reports on the results of a 6-year project funded by the Joint Food and Agriculture Organization of the United Nations/International Atomic Energy Agency (FAO/IAEA) Programme of Nuclear Techniques in Food and Agriculture entitled 'Enabling Technologies for the Expansion of the SIT for Old and New World Screwworm'. A major goal of the project was to better understand population genetic variation in screwworms as an aid to the identification of isolated populations. The project also addressed issues related to genetic sexing, cuticular hydrocarbons, population dynamics, genetic transformation and chromosome analysis.

Surveying Dead Trees and CO2-Induced Stressed Trees Using AVIRIS in the Long Valley Caldera

NASA Technical Reports Server (NTRS)

deJong, Steven M.

1996-01-01

Since 1980 the Long Valley Caldera in the eastern Sierra Nevada (California) has shown signs of renewed volcanic activity. Frequent earthquakes, a re-inflation of the caldera, hydrothermal activity and gas emissions are the outer symptoms of this renewed activity. In 1990 and 1991 several areas of dying trees were found around Mammoth Mountain. The cause of the die off of the trees was first sought in the persistent drought in the preceding years. However, the trees died regardless of age and species. Farrar et al. (1995) started a soil-gas survey in 1994 in the dead-tree areas and found carbon dioxide concentrations ranging from 30 to 96% at soil depths between 30 and 60 cm. CO2 concentrations in the atmosphere are usually around 0.03% and in the soil profile CO2 levels do commonly not exceed 4 to 5%. Although not much is known about the effect of high levels of carbon dioxide in the soil profile on roots, it is most likely that the trees are dying due to oxygen deprivation: the CO2 drives the oxygen out of the soil. So far, four sites of dead trees have been mapped around Mammoth Mountain. The two largest dying trees sites are located near Horseshoe Lake and near Mammoth Mountain Main Lodge covering approximately an area of 10 and 8 ha respectively. Analysis of the gas composition regarding the He-3/He-4 ratio and the percentage biogenic carbon reveals the source of the gas: the magma body beneath the Long Valley Caldera. Until recently it was not known that volcanoes release abundant carbon dioxide from their flanks as diffuse soil emanations. As a result of the magma gas emission around Mammoth Mountain there is an excellent sequence of dead trees, stressed trees, healthy trees and bare soil surfaces. This research site provides excellent opportunities to: (1) Study the capabilities of imaging spectrometry to map stressed (and dead) pine and fir species; (2) Study methods to separate the vivid vegetation, stressed vegetation and dead vegetation from the soil background of glacial deposits and crystalline rocks. The dead tree areas are located on the flanks of Mammoth Mountain (N:37 deg 37' 45" and W:119 deg 02' 05") at an elevation between 2600 and 3000 meters. The area is covered by an open type of Montane Forest. The dominant tree species are Lodgepole Pine (Pinus contorta), the Red Fir (Abies magnifica) and the Jeffrey Pine (Pinus jeffreyi). The soil surface near Horseshoe Lake is generally fairly bright. The surface is covered by glacial deposits (till) consisting mainly of weathered granitic rocks.

Discovery of Nascent Vents and Recent Colonization Associated with(Re)activated Hydrothermal Vent Fields by the GALREX 2011 Expedition on the Galápagos Rift

NASA Astrophysics Data System (ADS)

Shank, T. M.; Holden, J. F.; Herrera, S.; Munro, C.; Muric, T.; Lin, J.; Stuart, L.

2011-12-01

GALREX 2011 was a NOAA OER telepresence cruise that explored the diverse habitats and geologic settings of the deep Galápagos region. The expedition made12 Little Hercules ROV dives in July 2011.Abundant corals and a strong depth zonation of species (including deepwater coral communities) were found near 500 m depth on Paramount Seamount, likely influenced by past low sea level states, wave-cut terrace processes, and the historical presence of shallow reef structures. At fresh lava flows with associated (flocculent) hydrothermal venting near 88° W, now known as Uka Pacha and Pegasus Vent Fields, rocks were coated with white microbial mat and lacked sessile fauna, with few mobile fauna (e.g., bythograeid crabs, alvinocarid shrimp, polynoid worms, zoarcid fish, and dirivultid copepods). This suggests a recent creation of hydrothermal habitats through volcanic eruptions and/or diking events, which may have taken place over a 15 km span separating the two vent fields. The Rosebud vent field at 86°W was not observed and may have been covered with lava since last visited in 2005. A hydrothermal vent field near 86°W was discovered that is one of the largest vent fields known on the Rift (120m by 40m). Low-temperature vent habitats were colonized by low numbers of tubeworms including Riftia, Oasisia, and a potential Tevnia species (the latter not previously observed on the Galapagos Rift). Patches of tubeworms were observed with individuals less than 2cm in length, and the relatively few large Riftia had tube lengths near 70cm long. Large numbers of small (< 3cm long) bathymodiolin mussels lined cracks and crevices throughout the active part of the field. Live clams, at least four species of gastropod limpets, three species of polynoid polychaetes, juvenile and adult alvinocarid shrimp, actinostolid anemones, and white microbial communities were observed on the underside and vertical surfaces of basalt rock surfaces. There were at least 13 species of vent-endemic fauna. The active colonization was observed on relatively older basalt pillows and lobate lavas ringed by and amidst a large dead bed of Calyptogena clams (most with broken and dissolving shells greater than 25 cm in length, with a few of the same size living amongst the dissolving shells). Scattered pockets of living adult mussels were observed among these dead clams. The margins of the field were ringed with large numbers of dandelion siphonophores. This field, named Tempus Fugit Vent Field, was once a massive clam bed (> 20 years old) and now, while hosting mature mussel communities and adult clams (> 2 years old), is being actively colonized by vent-endemic fauna that can be considered to be recent arrivals and colonizers (less than a few months) at Galapagos vent fields. These findings not only provide strong evidence of recent volcanic activity between 85° W and 88° W on the Galapagos Rift, but provide evidence that the rates of hydrothermal habitat turnover via eruption, dike injection, or venting cessation may be considerably higher than previously thought along the Galápagos Rift.

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.

PubMed

Makarova, Kira S; Sorokin, Alexander V; Novichkov, Pavel S; Wolf, Yuri I; Koonin, Eugene V

2007-11-27

An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes. New Archaeal Clusters of Orthologous Genes (arCOGs) were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon) using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for identification of remote orthologs. The annotation of arCOGs is a consensus between three assignments based on the COGs, the CDD database, and the annotations of homologs in the NR database. The 7538 arCOGs, on average, cover approximately 88% of the genes in a genome compared to a approximately 76% coverage in COGs. The finer granularity of ortholog identification in the arCOGs is apparent from the fact that 4538 arCOGs correspond to 2362 COGs; approximately 40% of the arCOGs are new. The archaeal gene core (protein-coding genes found in all 41 genome) consists of 166 arCOGs. The arCOGs were used to reconstruct gene loss and gene gain events during archaeal evolution and gene sets of ancestral forms. The Last Archaeal Common Ancestor (LACA) is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for the last common ancestors of Crenarchaeota and Euryarchaeota, respectively. It is inferred that LACA was a chemoautotrophic hyperthermophile that, in addition to the core archaeal functions, encoded more idiosyncratic systems, e.g., the CASS systems of antivirus defense and some toxin-antitoxin systems. The arCOGs provide a convenient, flexible framework for functional annotation of archaeal genomes, comparative genomics and evolutionary reconstructions. Genomic reconstructions suggest that the last common ancestor of archaea might have been (nearly) as advanced as the modern archaeal hyperthermophiles. ArCOGs and related information are available at: ftp://ftp.ncbi.nih.gov/pub/koonin/arCOGs/.

Electron transfer to nitrogenase in different genomic and metabolic backgrounds.

PubMed

Poudel, Saroj; Colman, Daniel R; Fixen, Kathryn R; Ledbetter, Rhesa N; Zheng, Yanning; Pence, Natasha; Seefeldt, Lance C; Peters, John W; Harwood, Caroline S; Boyd, Eric S

2018-02-26

Nitrogenase catalyzes the reduction of dinitrogen (N 2 ) using low potential electrons from ferredoxin (Fd) or flavodoxin (Fld) through an ATP dependent process. Since its emergence in an anaerobic chemoautotroph, this oxygen (O 2 ) sensitive enzyme complex has evolved to operate in a variety of genomic and metabolic backgrounds including those of aerobes, anaerobes, chemotrophs, and phototrophs. However, whether pathways of electron delivery to nitrogenase are influenced by these different metabolic backgrounds is not well understood. Here, we report the distribution of homologs of Fds, Flds, and Fd/Fld-reducing enzymes in 359 genomes of putative N 2 fixers (diazotrophs). Six distinct lineages of nitrogenase were identified and their distributions largely corresponded to differences in the host cells' ability to integrate O 2 or light into energy metabolism. Predicted pathways of electron transfer to nitrogenase in aerobes, facultative anaerobes, and phototrophs varied from those in anaerobes at the level of Fds/Flds used to reduce nitrogenase, the enzymes that generate reduced Fds/Flds, and the putative substrates of these enzymes. Proteins that putatively reduce Fd with hydrogen or pyruvate were enriched in anaerobes, while those that reduce Fd with NADH/NADPH were enriched in aerobes, facultative anaerobes, and anoxygenic phototrophs. The energy metabolism of aerobic, facultatively anaerobic, and anoxygenic phototrophic diazotrophs often yields reduced NADH/NADPH that is not sufficiently reduced to drive N 2 reduction. At least two mechanisms have been acquired by these taxa to overcome this limitation and to generate electrons with potentials capable of reducing Fd. These include the bifurcation of electrons or the coupling of Fd reduction to reverse ion translocation. IMPORTANCE Nitrogen fixation supplies fixed nitrogen to cells from a variety of genomic and metabolic backgrounds including those of aerobes, facultative anaerobes, chemotrophs, and phototrophs. Here, using informatics approaches applied to genomic data, we show that pathways of electron transfer to nitrogenase in metabolically diverse diazotrophic taxa have diversified primarily in response to host cells' acquired ability to integrate O 2 or light into their energy metabolism. Acquisition of two key enzyme complexes enabled aerobic and facultatively anaerobic phototrophic taxa to generate electrons of sufficiently low potential to reduce nitrogenase: the bifurcation of electrons via the Fix complex or the coupling of Fd reduction to reverse ion translocation via the Rhodobacter nitrogen fixation (Rnf) complex. Copyright © 2018 American Society for Microbiology.

Methane fates in the benthos and water column at cold seep sites along the continental margin of Central and North America

NASA Astrophysics Data System (ADS)

Hansman, Roberta L.; Thurber, Andrew R.; Levin, Lisa A.; Aluwihare, Lihini I.

2017-02-01

The potential influence of methane seeps on carbon cycling is a key question for global assessments, but the study of carbon cycling in surface sediments and the water column of cold seep environments is complicated by the high temporal and spatial variability of fluid and gas fluxes at these sites. In this study we directly examined carbon sources supporting benthic and planktonic food webs at venting methane seeps using isotopic and molecular approaches that integrate this variability. At four seep environments located along North and Central America, microorganisms from two size fractions were collected over several days from 2800 to 9050 l of seawater to provide a time-integrated measure of key microbial groups and the carbon sources supporting the overall planktonic microbial community. In addition to water column measurements, the extent of seafloor methane release was estimated at two of the sites by examining the stable carbon isotopic signature (δ13C) of benthic metazoan infauna. This signature reveals carbon sources fueling the base of the food chain and thus provides a metric that represents a time-integrated view of the dominant microbial processes within the sediment. The stable carbon isotopic composition of microbial DNA (δ13C-DNA), which had values between -17.0 and -19.5‰, indicated that bulk planktonic microbial production was not ultimately linked to methane or other 13C-depleted seep-derived carbon sources. Instead these data support the importance of organic carbon derived from either photo- or chemoautotrophic CO2 fixation to the planktonic food web. Results of qPCR of microbial DNA sequences coding for a subunit of the particulate methane monooxygenase gene (pmoA) showed that only a small percentage of the planktonic microbial community were potential methane oxidizers possessing pmoA (<5% of 16S rRNA gene copies). There was an overall decrease of 13C-depleted carbon fueling the benthic metazoan community from 3 to 5 cm below the seafloor to the sediment surface, reflecting limited use of isotopically depleted carbon at the sediment surface. Rare methane emission as indicated by limited aerobic methane oxidation acts to corroborate our findings for the planktonic microbial community.

By more ways than one: Rapid convergence at hydrothermal vents shown by 3D anatomical reconstruction of Gigantopelta (Mollusca: Neomphalina).

PubMed

Chen, Chong; Uematsu, Katsuyuki; Linse, Katrin; Sigwart, Julia D

2017-03-01

Extreme environments prompt the evolution of characteristic adaptations. Yet questions remain about whether radiations in extreme environments originate from a single lineage that masters a key adaptive pathway, or if the same features can arise in parallel through convergence. Species endemic to deep-sea hydrothermal vents must accommodate high temperature and low pH. The most successful vent species share a constrained pathway to successful energy exploitation: hosting symbionts. The vent-endemic gastropod genus Gigantopelta, from the Southern and Indian Oceans, shares unusual features with a co-occurring peltospirid, the 'scaly-foot gastropod' Chrysomallon squamiferum. Both are unusually large for the clade and share other adaptive features such as a prominent enlarged trophosome-like oesophageal gland, not found in any other vent molluscs. Transmission electron microscopy confirmed endosymbiont bacteria in the oesophageal gland of Gigantopelta, as also seen in Chrysomallon. They are the only known members of their phylum in vent ecosystems hosting internal endosymbionts; other vent molluscs host endosymbionts in or on their gills, or in the mantle cavity. A five-gene phylogenetic reconstruction demonstrated that Gigantopelta and Chrysomallon are not phylogenetically sister-taxa, despite their superficial similarity. Both genera have specialist adaptations to accommodate internalised endosymbionts, but with anatomical differences that indicate separate evolutionary origins. Hosting endosymbionts in an internal organ within the host means that all resources required by the bacteria must be supplied by the animal, rather than directly by the vent fluid. Unlike Chrysomallon, which has an enlarged oesophageal gland throughout post-settlement life, the oesophageal gland in Gigantopelta is proportionally much smaller in juveniles and the animals likely undergo a trophic shift during ontogeny. The circulatory system is hypertrophied in both but the overall size is smaller in Gigantopelta. In contrast with Chrysomallon, Gigantopelta possesses true ganglia and is gonochoristic. Key anatomical differences between Gigantopelta and Chrysomallon demonstrate these two genera acquired a similar way of life through independent and convergent adaptive pathways. What appear to be the holobiont's adaptations to an extreme environment, are driven by optimising bacteria's access to vent nutrients. By comparing Gigantopelta and Chrysomallon, we show that metazoans are capable of rapidly and repeatedly evolving equivalent anatomical adaptations and close-knit relationships with chemoautotrophic bacteria, achieving the same end-product through parallel evolutionary trajectories.

A multiproxy approach to understanding the "enhanced" flux of organic matter through the oxygen deficient waters of the Arabian Sea

NASA Astrophysics Data System (ADS)

Keil, R. G.; Neibauer, J.; Biladeau, C.; van der Elst, K.; Devol, A. H.

2015-10-01

Free-drifting sediment net traps were deployed 14 times at depths between 80 and 500 m for 1-3 days each during the late monsoon/intermonsoon transition in the central Arabian Sea. Two locations (19.5 and 15.5° N) were within the permanently oxygen deficient zone, and a third (11° N) had a shallow and thin oxygen minimum. The secondary nitrite maximum, which serves as a tracer of the oxygen deficient zone (ODZ) zone, thinned from ∼ 250 m thick at stations 19.5 and 15.5° N to ∼ 50 m thick at station 11° N. Overall, organic carbon fluxes ranged from 13.2 g m2 yr-1 at 80 m to a minimum of 1.1 g m2 yr-1 at 500 m. Fluxes at the more oxygenated 11° N station attenuate faster than within the permanent ODZ. Martin curve attenuation coefficients for 19.5 and 15.5° N are 0.59 and 0.63 and for 11° N it is 0.98. At least six potential mechanisms might explain why sinking particles sinking through the ODZ are more effectively transferred to depth; (M1) oxygen effects, (M2) microbial loop efficiencies and chemoautotrophy, (M3) changes in zooplankton dynamics, (M4) additions of ballast that might sorb and protect organic matter from decay, (M5) inputs of refractory organic matter, and (M6) changes in sinking speeds. These mechanisms are intertwined, and were explored using a combination of mineral (XPS) and organic matter characterizations of the sinking material and ship-board incubation experiments. Evidence was found supporting an oxygen effect and/or changes in the efficiency of the microbial loop including the addition of chemoautotrophic carbon to the sinking flux in the upper 500 m. Less evidence was found for the other potential mechanisms. A simple conceptual model consistent with our and other recent data suggests that the upper ODZ microbial community determines the initial flux attenuation, and that deeper in the water column zooplankton and sinking speed become more important. The exact interplay between the various mechanisms remains to be further evaluated.

A multiproxy approach to understanding the "enhanced" flux of organic matter through the oxygen-deficient waters of the Arabian Sea

NASA Astrophysics Data System (ADS)

Keil, Richard G.; Neibauer, Jacquelyn A.; Biladeau, Christina; van der Elst, Kelsey; Devol, Allan H.

2016-04-01

Free-drifting sediment net traps were deployed 14 times at depths between 80 and 500 m for 1-3 days each during the late monsoon-intermonsoon transition in the central Arabian Sea. Two locations (19.5 and 15.5° N) were within the permanently oxygen-deficient zone (ODZ), and a third (11° N) had a shallow and thin oxygen minimum. The secondary nitrite maximum, which serves as a tracer of the ODZ, thinned from ˜ 250 m thick at stations 19.5 and 15.5° N to ˜ 50 m thick at station 11° N. Overall, organic carbon fluxes ranged from 13.2 g m2 yr-1 at 80 m to a minimum of 1.1 g m2 yr-1 at 500 m. Fluxes at the more oxygenated 11° N station attenuate faster than within the permanent ODZ. Martin curve attenuation coefficients for 19.5 and 15.5° N are respectively 0.59 and 0.63 and for 11° N it is 0.98. At least six potential mechanisms might explain why particles sinking through the ODZ are more effectively transferred to depth: (M1) oxygen effects, (M2) microbial loop efficiencies and chemoautotrophy, (M3) changes in zooplankton dynamics, (M4) additions of ballast that might sorb and protect organic matter from decay (M4a) or change sinking speeds (M4b), (M5) inputs of refractory organic matter and (M6) temperature effects. These mechanisms are intertwined, and they were explored using a combination of mineral (XPS) and organic matter characterizations of the sinking material, shipboard incubation experiments, and evaluations of existing literature. Direct evidence was found supporting an oxygen effect and/or changes in the efficiency of the microbial loop including the addition of chemoautotrophic carbon to the sinking flux in the upper 500 m. Less direct evidence was found for the other potential mechanisms. A simple conceptual model consistent with our and other recent data suggests that the upper ODZ microbial community determines the initial flux attenuation, and that zooplankton and sinking speed become more important deeper in the water column. The exact interplay between the various mechanisms remains to be further evaluated.

Faunal and stable isotopic analyses of benthic foraminifera from the Southeast Seep on Kimki Ridge offshore southern California, USA

USGS Publications Warehouse

McGann, Mary; Conrad, James E.

2018-01-01

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 δ13C 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 δ13C 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 δ13C 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.

Methane seepage along the Hikurangi Margin offshore New Zealand: 6 years of multidisciplinary studies

NASA Astrophysics Data System (ADS)

Greinert, J.; Bialas, J.; Klaucke, I.; Crutchley, G.; Dale, A.; Linke, P.; Sommer, S.; Bowden, D.; Rowden, A.; de Haas, H.; de Stigter, H.; Faure, K.

2012-12-01

Detailed studies in 2006, 2007 and 2011 along the east coast of New Zealand's North Island highlighted the close link of sub-bottom fluid pathways and seafloor expressions of methane seepage such as clam fields, carbonate build-ups, tubeworms, bacterial mats and methane release (Marine Geology 272). Prior to our studies, only accidental observations of hydroacoustic anomalies, recoveries of calyptogena shells and methane-derived carbonate chimneys indicated active seepage. Wide areas of the sub-seafloor show BSR structures, gas migration pathways, gas chimneys and blanking zones, which are closely linked to actual seep sites. Sidescan surveys showed four prominent seep areas at Omakere Ridge in 1120m water depth, three of them perfectly matching the shapes and locations of faults seen in high resolution 3D-seismic surveys. The fourth seep, Bear's Paw, on its western side represents an old seep which developed into a cold water coral habitat. At the actively seeping eastern part, gas hydrates could be retrieved and bubble release was observed hydroacoustically and confirmed by high dissolved methane values (380nM). No strong microbial oxidation effects could be found in δ13C values plotting along a mixing curve between pure seep (-70 ‰PDB) and atmospheric methane (-47 ‰PDB). Lander deployments show a tide-influenced gas discharge with sometimes eruptive bubble release with possible plume development transporting methane-charged water higher up into the water column. Rock Garden, with just above 600m water depth at its top outside the gas hydrate stability zone, hosts two main seep areas. ROV observations at Faure Site document eruptive releases of free gas from decimeter-wide craters at the seafloor. Flux estimates show peak releases of 420ml/min with bubbles up to 9mm in diameter. Concentrations of dissolved methane reach up to 3500nM close to the bottom, but higher concentrations are limited to below 400m of water depth; here, methane is transported towards the sea surface or even into the mixed layer. Faure site is just at the limit of the gas hydrate phase boundary, where relatively high-permeable sediment layers act as preferred pathway for fluids from below a shallow BSR. Seismic studies at the seep site LM-3 show gas chimneys as main fluid migration pathways in the sub-seafloor. Opouawe Bank has the densest occurrence of seeps. In water depths between 800 and 1200m, seeps of different ages and appearances exist in close proximity. North and South Tower resemble old structures with massive aragonitic carbonate blocks paving the seafloor, tube worms, bacterial mats, clams and beds of ampharetid polychaetes. These patchy polychaetes habitats have a very high total oxygen uptake of up to 83.7 mmol m^-2 day^-1) feeding from organic carbon generated via aerobic methane oxidation. Hydroacoustic flares at the 1200m deep Towers rise more than 600m into the water column above, which the dissolved gas concentrations quickly drop to background. In contrast, the isolated Takahe seep only 2 miles away shows no carbonates at the seafloor surface despite a well developed acoustic gas chimney and surface-near gas hydrates. This seep represents a much younger seep which highlights the great spatial and temporal variability in seep occurrences and activity, which can also be found in fossil seeps on land.

DUSEL and the future of deep terrestrial microbiology (Invited)

NASA Astrophysics Data System (ADS)

Onstott, T. C.; Peters, C. A.; Murdoch, L. C.; Elsworth, D.; Sonnenthal, E. L.; Kieft, T.; Boutt, D. F.; Germanovich, L.; Glaser, S. D.; Wang, H. F.; Roggenthen, B.; Lesko, K.; Cushman, P.; Stetler, L. D.; Bang, S.; Anderson, C.

2009-12-01

DUSEL will take advantage of the existing subsurface architecture of the deepest mine in the U.S. to provide a platform for launching new exploration into the deep terrestrial biosphere. Multi-year experiments are currently being designed to delineate the relationships between microbial diversity and activity and hydraulic connectivity, temperature, pressure, strain rate and multiphase fluids. Unlike the physics experiments, which will be located close to the center of the mine, most of these experiments will be located at the periphery in existing tunnels at 100 to 2400 m depth in order to access fluid fill fractures with boreholes. Hydrological models suggest that DUSEL could sample ~100 km3 volume for microbial biogeographic and transport studies. The high-capacity underground water filtration plant used to generate ultrapure water for neutrino detectors will readily supply water for microbiology coring projects reducing microbial contamination. This will be essential for the drilling platform located at 2400 m depth that will drill down to 7+ km and 120oC in search of the upper temperature limit for life. Another advantage of underground coring is that the drilling fluid pressure will be much less than that of the fracture water, which means that when the coring bit intersects a water-filled fracture, the fracture water will flow into the core barrel reducing the contamination of fracture surfaces in the cores. The ultra-low radiation background counting facility to be located at 1475 m depth will potentially enable 106 times improvement in the detection limit for subsurface microbial respiration rates using radioactive tracers. The Coupled Thermal-Hydrological-Mechanical-Chemical-Biological, block-heating experiment will examine how the microbial communities within fractures respond to the increased thermal and fluid flux. The Fracture Processes Facility is not only designed to determine what controls rock strength, but could also determine to what extent subsurface chemoautotrophic activity is regulated by tectonic episodicity. The DUSEL CO2 Facility will investigate how microbial activity is impacted by CO2 injection and whether microbial activity has a significant impact upon long-term sequestration of CO2. These three experiments represent a subset of the integrated suite of experiments planned for the first 5 years, but many more microbial experiments can be accommodated within DUSEL. With its unique experimental assets, km-scale spatial access and multi-decade observational lifetime, DUSEL will usher in the next generation of exploration into the deep terrestrial biosphere and not only reveal the answers to many of its well-hidden secrets, but perhaps to the origin of life itself.

Organic and Inorganic Carbon in the Rio Tinto (Spain) Deep Subsurface System: a Possible Model for Subsurface Carbon and Lithoautotrophs on Mars.

NASA Astrophysics Data System (ADS)

Bonaccorsi, R.; Stoker, C. R.; MARTE Science Team

2007-12-01

The subsurface is the key environment for searching for life on planets lacking surface life. Subsurface ecosystems are of great relevance to astrobiology including the search for past/present life on Mars. Conditions on the Martian surface do not support biological activity but the subsurface might preserve organics and host subsurface life [1]. A key requirement for the analysis of subsurface samples on Mars is the ability to characterize organic vs. inorganic carbon pools. This information is needed to determine if the sample contains organic material of biological origin and/ or to establish if pools of inorganic carbon can support subsurface biospheres. The Mars Analog Rio Tinto Experiment (MARTE) performed deep drilling of cores i.e., down to 165-m depth, in a volcanically-hosted-massive-sulfide deposit at Rio Tinto, Spain, which is considered an important analog of the Sinus Meridiani site on Mars. Results from MARTE suggest the existence of a relatively complex subsurface life including aerobic and anaerobic chemoautotrophs, and strict anaerobic methanogens sustained by Fe and S minerals in anoxic conditions, which is an ideal model analog for a deep subsurface Martian environment. We report here on the distribution of organic (C-org: 0.01-0.3Wt% and inorganic carbon (IC = 0.01-7.0 Wt%) in a subsurface rock system including weathered/oxidized i.e., gossan, and unaltered pyrite stockwork. Cores were analyzed from 3 boreholes (BH-4, BH-7, and BH-8) that penetrated down to a depth of ~165 m into massive sulfide. Nearsurface phyllosilicate rich-pockets contain the highest amounts of organics (0.3Wt%) [2], while the deeper rocks contain the highest amount of carbonates. Assessing the amount of C pools available throughout the RT subsurface brings key insight on the type of trophic system sustaining its microbial ecosystem (i.e., heterotrophs vs. autotrophs) and the biogeochemical relationships that characterize a new type of subsurface biosphere at RT. This potentially novel biosphere on Earth could be used as a model to test for extant and extinct life on Mars. Furthermore, having found carbonates in an hyperacidic system (pH ~2.3) brings new insights on the possible occurrence of deep carbonates deposits under low-pH condition on Mars. [1] Boston, P.J., et al., 1992. Icarus 95,300-308; Bonaccorsi, Stoker and Sutter, 2007 Accepted with review in Astrobiology.

Sediment chemoautotrophy in the coastal ocean

NASA Astrophysics Data System (ADS)

Vasquez-Cardenas, Diana; Meysman, Filip J. R.; van Breugel, Peter; Boschker, Henricus T. S.

2016-04-01

A key process in the biogeochemistry of coastal sediments is the reoxidation of reduced intermediates formed during anaerobic mineralization which in part is performed by chemoautotrophic micro-organisms. These microbes fix inorganic carbon using the energy derived from reoxidation reactions and in doing so can fix up to 32% of the CO2 released by mineralization. However the importance and distribution of chemoautotrophy has not been systematically investigated in these environments. To address these issues we surveyed nine coastal sediments by means of bacterial biomarker analysis (phospholipid derived fatty acids) combined with stable isotope probing (13C-bicarbonate) which resulted in an almost doubling of the number of observations on coastal sedimentary chemoautotrophy. Firstly, sediment chemoautotrophy rates from this study and rates compiled from literature (0.07 to 36 mmol C m-2 d-1) showed a power-law relation with benthic oxygen uptake (3.4 to 192 mmol O2 m-2 d-1). Benthic oxygen uptake was used as a proxy for carbon mineralization to calculate the ratio of the CO2 fixed by chemoautotrophy over the total CO2 released through mineralization. This CO2 efficiency was 3% in continental shelf, 9% in nearshore and 21% in salt marsh sediments. These results suggest that chemoautotrophy plays an important role in C-cycling in reactive intertidal sediments such as salt marshes rather than in the organic-poor, permeable continental shelf sediments. Globally in the coastal ocean our empirical results show that chemoautotrophy contributes ˜0.05 Pg C y-1 which is four times less than previous estimates. Secondly, five coastal sediment regimes were linked to the depth-distribution of chemoautotrophy: 1) permeable sediments dominated by advective porewater transport, 2) bioturbated sediments, and cohesive sediments dominated by diffusive porewater transport characterized by either 3) canonical sulfur oxidation, 4) nitrate-storing Beggiatoa, or 5) electrogenic sulfur oxidation. Sediments with an O2-H2S interface exhibited highest chemoautotrophy activity in the top centimeter via canonical sulfur oxidation, whereas in the presence of electrogenic sulfur oxidation a uniform distribution of chemoautotrophy throughout the top centimeters of the sediment was evidenced. Lowest dark carbon fixation was found in permeable advective-driven sediments with deep oxygen penetration resulting in higher subsurface than surface activity. Hence, the depth-distribution of chemoautotrophy in coastal sediments varies due to several biogeochemical characteristics such as grain size, organic carbon content, presence of filamentous sulfur oxidizing bacteria, and macrofaunal activity.

Sulfide as a Chemoautotrophic Electron Donor for Dissimilatory Arsenate Reduction in Mono Lake, California

NASA Astrophysics Data System (ADS)

Hoeft, S. E.; Kulp, T. R.; Stolz, J. S.; Oremland, R. S.

2003-12-01

In aqueous systems, arsenic occurs as arsenate [As(V)] or as arsenite [As(III)], with the latter form being more toxic and mobile. Mono Lake, California is a meromictic soda lake (pH = 9.8; salinity = 70-90 g/L) with exceptionally high arsenic content ( ˜200 μ M), a consequence of hydrothermal inputs combined with evaporative concentration. Previous work has shown that arsenic speciation changes from As(V) to the more reduced As(III) with vertical transition from the lake's surface oxic waters to its unmixed, anoxic bottom waters and that dissimilatory reduction is responsible for the observed change in arsenic speciation. Rates of in situ dissimilatory As(V) reduction measured by radiotracer ( ˜1- 6 μ mol/L/d) were estimated to be significant enough to mineralize up to 14% of annual primary productivity. Subsequent lab-based investigations with As(V)-amended ( ˜1-2 mM) bottom water displayed significantly higher rates (150-260 μ mol/L/d) of As(V) reduction and were not limited by the availability of organic electron donors such as acetate, lactate, malate and glucose. The focus of this study was to identify a natural source of electrons for As(V) reduction in Mono Lake. While Mono Lake contains plentiful dissolved organic carbon ( ˜7 mM) this material is usually refractory and resistant to bacterial oxidation. Alternatively, the anoxic bottom waters contain high concentrations of sulfide ions ( ˜1-2 mM) that could potentially serve as an electron donor for dissimilatory As(V) reduction. In a time course experiment with As(V)-amended Mono Lake bottom water, we observed oxidation of sulfide linked to the reduction of As(V) to As(III). This reaction did not occur in filter sterilized controls and sulfide loss did not occur in samples lacking As(V). In bottom water amended with additional sulfide (total = 6 mM) and As(V), we observed a linear relationship between rates of dissimilatory As(V) reduction and As(V) concentration. The highest rate observed under these conditions was ˜3 mmol/L/d, over 1000-fold higher than Mono Lake in situ rates. We isolated an anaerobic bacterium from Mono Lake bottom water, strain MLMS-1, that grows in mineral salts media by oxidizing sulfide to sulfate and reducing As(V) to As(III). MLMS-1 grew with a 4:1 stoichiometry of As(V) reduced to sulfide oxidized, indicating an 8 electron transfer. MLMS-1 aligned by 16S rDNA amplification and sequencing in the δ -Proteobacteria, being closely related to the sulfate-reducing bacteria of the genus Desulfobulbus. However, strain MLMS-1 does not grow with sulfate as an electron acceptor.

Methane and Dissolved Organic Carbon Sustain an Ecosystem within a Density Stratified Coastal Aquifer of the Yucatan Peninsula, Mexico. Evidence for a Subterranean Microbial Loop?

NASA Astrophysics Data System (ADS)

Brankovits, David; Pohlman, John W.; Niemann, Helge; Leigh, Mary Beth; Casso, Michael; Alvarez Noguera, Fernando; Lehmann, Moritz F.; Iliffe, Thomas M.

2016-04-01

In coastal karst terrains, anchialine caves that meander in density stratified aquifers provide an exceptional opportunity for scientists to study in situ biogeochemical processes within the groundwater. The Caribbean coast of Mexico's Yucatan Peninsula contains over 1000 km of mapped cave passages, the densest known accumulation of anchialine caves in the world. A decades-old study based on the simple observation of 13C-depleted biomass in the cave-adapted fauna suggested biogeochemical processes related to methane-linked carbon cycling and/or other chemoautotrophic pathways as a source of energy and carbon. In this study, we utilized cave diving and a novel sampling device (the Octopipi) to obtain cm-scale water column profiles of methane, DOC and DIC concentrations and stable carbon isotope ratios to identify the energy sources and microbial processes that sustain life in these subterranean estuaries. High concentrations (up to 9522 nM) low-δ13C (as low as -67.5 permil) methane near the ceiling of the cave (in the fresh water section of the stratified water column) and evidence for methane oxidation in the brackish water portion of the water column suggest methane availability and consumption. Profiles obtained by the Octopipi demonstrate that virtually all of the methane (˜99%) is oxidized at the interface of anoxic freshwater and hypoxic brackish water masses. The high-methane water mass near the ceiling also contained elevated concentrations of DOC (851 μM) that displayed comparatively high δ13C (-27.8 to -28.2 permil), suggesting terrestrial organic matter input from the overlying soils. Low-methane brackish and saline water was characterized by lower DOC concentration (15 to 97 μM), yet with similar δ13C (-25.9 to -27.2 permil), suggesting significant terrestrial organic matter consumption or removal with increasing depth, from fresh to saline water, within the water column. The presence of 13C-depleted fatty acids (e.g., C16:1ω7c with δ13C-values as low as -54.1 permil) and deuterium-depleted δD values (e.g., as low as δD = -225 permil) from tissues of cave-adapted shrimps suggest that methanotrophic bacteria contributed a substantial fraction of their diet. Molecular microbial community analyses are underway to identify the taxonomic associations and syntrophy effects within a subterranean microbial loop that provides carbon and energy to the anchialine food web. These findings provide novel insight into the carbon cycle and methane dynamics for a largely unknown, yet widespread coastal habitat beneath the Earth's surface.

Carbon sequestration in soybean crop soils: the role of hydrogen-coupled CO2 fixation

NASA Astrophysics Data System (ADS)

Graham, A.; Layzell, D. B.; Scott, N. A.; Cen, Y.; Kyser, T. K.

2011-12-01

Conversion of native vegetation to agricultural land in order to support the world's growing population is a key factor contributing to global climate change. However, the extent to which agricultural activities contribute to greenhouse gas emissions compared to carbon storage is difficult to ascertain, especially for legume crops, such as soybeans. Soybean establishment often leads to an increase in N2O emissions because N-fixation leads to increased soil available N during decomposition of the low C:N legume biomass. However, soybean establishment may also reduce net greenhouse gas emissions by increasing soil fertility, plant growth, and soil carbon storage. The mechanism behind increased carbon storage, however, remains unclear. One explanation points to hydrogen coupled CO2 fixation; the process by which nitrogen fixation releases H2 into the soil system, thereby promoting chemoautotrophic carbon fixation by soil microbes. We used 13CO2 as a tracer to track the amount and fate of carbon fixed by hydrogen coupled CO2 fixation during one-year field and laboratory incubations. The objectives of the research are to 1) quantify rates of 13CO2 fixation in soil collected from a field used for long-term soybean production 2) examine the impact of H2 gas concentration on rates of 13CO2 fixation, and 3) measure changes in δ13C signature over time in 3 soil fractions: microbial biomass, light fraction, and acid stable fraction. If this newly-fixed carbon is incorporated into the acid-stable soil C fraction, it has a good chance of contributing to long-term soil C sequestration under soybean production. Soil was collected in the field both adjacent to root nodules (nodule soil) and >3cm away (root soil) and labelled with 13CO2 (1% v/v) in the presence and absence of H2 gas. After a two week labelling period, δ13C signatures already revealed differences in the four treatments of bulk soil: -17.1 for root, -17.6 for nodule, -14.2 for root + H2, and -6.1 for nodule + H2. Labelled soil was then placed in nylon mesh bags and buried in the field at a depth of 15cm in a soybean field at the Central Experiment Farm in Ottawa, Ontario. Samples will be removed at intervals of 1,2,3,6,9,12, and 15 months, and the δ13C of three soil fractions will be examined to reveal changes in carbon storage over time. Our results will provide insights into the fate of carbon fixed during hydrogen coupled CO2 fixation, and demonstrate whether this CO2 fixation can contribute to the long-term greenhouse gas balance of soybean production systems.

The Arsenic Cycle in Searles Lake, California: An Arsenic-Rich, Salt-Saturated Soda Lake. II. Isolation of Arsenic-Metabolizing Microbes.

NASA Astrophysics Data System (ADS)

Switzer Blum, J.; Hoeft, S. E.; Stolz, J. F.; Langley, S.; Beveridge, T. J.; Kulp, T. R.; Oremland, R. S.

2004-12-01

The motivation for isolating arsenic-metabolizing prokaryotes from Searles Lake was to characterize the physiology of microbes that can cope simultaneously with at least 3 environmental extremes: saturating salt concentration, high pH, and high dissolved inorganic arsenic. A secondary motivation was to find extremely halophilc Archaea that could respire As(V), as this has only been reported for the Crenarchaea. Enrichment cultures of arsenate [As(V)]-respirers were established by inoculating Searles Lake mud into an anaerobic, alkaline (pH = 9.8) artificial medium containing 346 g/L dissolved salts, with lactate as the electron donor and As(V) as the electron acceptor. After about 6 months of bi-weekly transfers, the enrichment was purified by serial dilution, with the highest growth-positive dilution tube exhibiting motile cells having uniform morphology (curved rods). This culture, strain SLAS-1, grew by oxidizing lactate to acetate plus carbon dioxide while reducing As(V) to arsenite [As(III)]. The doubling time was 48 hours at 346 g/L salinity, and nearly equivalent growth rates were observed over a salinity range of 200 to 346 g/l, with no growth evident below 200 g/L. The pH range was 8.5 to 10, with an optimum at 9.5. Strain SLAS-1 has an unusual motility that can be characterized as a "fish-like" swimming motion. Thin section electron micrographs revealed the presence of an internal cytoplasmic filament that runs the full length of the microorganism. We suggest that this filament may be involved in cellular motility. However, taxonomic classification of SLAS-1 made by 16S rRNA gene sequences aligned it in the order Haloanaerobacteriales of the Domain Bacteria. In a further effort to isolate haloalkaliphilic Archaea, a similar enrichment strategy was employed as above, but cell-wall antibiotics were added to the medium to discourage the growth of Bacteria. An enrichment culture, designated Serl-Ab, was established that oxidized lactate to acetate plus carbon dioxide. Preliminary evidence suggests that the culture consists of a lactate-oxidizing sulfate-reducer growing in synthrophy with a chemoautotrophic, sulfide-oxidizing As(V)-respirer. Terminal restriction length polymorphism analysis has indicated the presence of both bacterial and archaeal components in the Serl-Ab enrichment, although it is not yet known which is responsible for the observed As(V)-reduction and sulfate-reduction. Efforts are ongoing to resolve Serl-Ab by using classical isolation procedures for a heterotrophic sulfate reducer and an autotrophic As(V)-respirer. In addition, new efforts are being undertaken to isolate hydrogen-oxidizing As(V)-respirers, as well as aerobic As(III)-oxidizers from the extreme environment of Searles Lake.

Satellites of giant planets — possible sites for origin and existence of biospheres

NASA Astrophysics Data System (ADS)

Simakov, Michael B.

All giant planets of the Solar system have a big number of satellites (61 of Jupiter, 52 of Saturn, known in 2003). A small part of them consist very large bodies, quite comparable to planets of terrestrial type, but including very significant share of water ice. Some from them have an atmosphere. E.g., the mass of a column of the Titan’s atmosphere exceeds 15 times the mass of the Earth atmosphere column. Formation (or capture) of satellites is a natural phenomenon, and satellite systems definitely should exist at extrasolar planets. As an example, we can see on Titan, the largest satellite of Saturn, which has a dense nitrogen atmosphere and a large quantity of liquid water under ice cover and so has a great exobiological significance. The most recent models of the Titan’s interior lead to the conclusion that a substantial liquid layer exists today under relatively thin ice cover inside Titan. The putative internal water ocean along with complex atmospheric photochemistry provide some exobiological niches on this body: (1) an upper layer of the internal water ocean; (2) pores, veins, channels and pockets filled with brines inside of the lowest part of the icy layer; (3) the places of cryogenic volcanism; (4) set of caves in icy layer connecting with cryovolcanic processes; (5) the brine-filled cracks in icy crust caused by tidal forces; (6) liquid water pools on the surface originated from meteoritic strikes; (7) the sites of hydrothermal activity on the bottom of the ocean. We can see all conditions needed for origin and evolution of biosphere — liquid water, complex organic chemistry and energy sources for support of biological processes — are on the Saturnian moon. Galileo spacecraft has given indications, primarily from magnetometer and gravity data, of the possibility that three of Jupiter’s four large moons, Europa, Ganymede and Callisto have such oceans also. The existing of liquid water ocean within icy world can be consequences of the physical properties of water ice, and they neither require the addition of antifreeze substances nor any other special conditions. On Earth life exists in all niches where water exists in liquid form for at least a portion of the year. Possible metabolic processes, such as nitrate/nitrite reduction, sulfate reduction and methanogenesis could be suggested for internal oceans of Titan and Jovanian satellites. Excreted products of the primary chemoautotrophic organisms could serve as a source for other types of microorganisms (heterotrophes). Subglacial life may be widespread among such planetary bodies as satellites of extrasolar giant planets, detected in our Galaxy.

Quantification of microbial activity in subsurface environments using a hydrogenase enzyme assay

NASA Astrophysics Data System (ADS)

Adhikari, R. R.; Nickel, J.; Kallmeyer, J.

2012-04-01

The subsurface biosphere is the largest microbial ecosystem on Earth. Despite its large size and extensive industrial exploitation, very little is known about the role of microbial activity in the subsurface. Subsurface microbial activity plays a fundamental role in geochemical cycles of carbon and other biologically important elements. How the indigenous microbial communities are supplied with energy is one of the most fundamental questions in subsurface research. It is still an enigma how these communities can survive with such recalcitrant carbon over geological time scales. Despite its usually very low concentration, hydrogen is an important element in subsurface environments. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways; they either obtain protons from the radiolysis of water and/or cleavage of hydrogen generated by the alteration of basaltic crust, or they dispose of protons by formation of water. Hydrogenase (H2ase) is a ubiquitous intracellular enzyme that catalyzes the interconversion of molecular hydrogen and/or water into protons and electrons. The protons are used for the synthesis of ATP, thereby coupling energy-generating metabolic processes to electron acceptors such as carbon dioxide or sulfate. H2ase activity can therefore be used as a measure for total microbial activity as it targets a key metabolic compound rather than a specific turnover process. Using a highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey and in marine subsurface sediments of the Barents Sea. Additionally, sulfate reduction rates (SRRs) were measured to compare the results of the H2ase enzyme assay with the quantitatively most important electron acceptor process. H2ase activity was found at all sites, measured values and distribution of activity varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from ca. 20 mmol H2 cm-3 d-1 close to the sediment-water interface to 0.5 mmol H2 cm-3 d-1 at a depth of 0.8 m. In samples from the Barents Sea H2ase activity ranged between 0.1 to 2.5 mmol H2 cm-3 d-1 down to a depth of 1.60 m. At all sites the SRR profile followed the H2ase activity profile until SRR declined to values close to the minimum detection limit (~10 pmol cm-3 d-1). H2ase activity increased again after SRR declined, indicating that other microbial processes are becoming quantitatively more important. The H2ase and SRR data show that our assay has a potential to become a valuable tool to measure total subsurface microbial activity.

Subsurface Organics in Aseptic Cores From the MARTE Robotic Drilling Experiment: Ground truth and Contamination Issues

NASA Astrophysics Data System (ADS)

Bonaccorsi, R.; Stoker, C. R.

2006-12-01

The subsurface is the key environment for searching for life on planets lacking surface life. This includes the search for past/present life on Mars where possible subsurface life could exist [1]. The Mars-Analog-Rio-Tinto-Experiment (MARTE) performed a simulation of a Mars robotic drilling at the RT Borehole#7 Site ~6.07m, atop a massive-pyrite deposit from the Iberian Pyritic Belt. The RT site is considered an important analog of Sinus Meridiani on Mars, an ideal model analog for a subsurface Martian setting [2], and a relevant example of deep subsurface microbial community including aerobic and anaerobic chemoautotrophs [4-5]. Searching for microbes or bulk organics of biological origin in a subsurface sample from a planet is a key scientific objective of Robotic drilling missions. During the 2005 Field experiment 28 minicores were robotically handled and subsampled for life detection experiments under anti-contamination protocols. Ground truth included visual observation of cores and lab based Elemental and Isotope Ratios Mass Spectrometry analysis (EA-IRMS) of bulk organics in Hematite and Gohetite-rich gossanized tuffs, gossan and clay layers within 0-6m-depth. C-org and N-tot vary up to four orders of magnitude among the litter (~11Wt%, 0-1cm) and the mineralized (~3Wt%, 1-3cm) layers, and the first 6 m-depth (C-org=0.02-0.38Wt%). Overall, the distribution/ preservation of plant and soil-derived organics (d13C-org = 26 per mil to 24 per mil) is ten times higher (C-org=0.33Wt%) that in hematite-poor clays, or where rootlets are present, than in hematite- rich samples (C-org=<0.01Wt%). This is consistent with ATP assay (Lightning-MVP, Biocontrol) for total biomass in subsurface (Borehole#7 ~6.07m, ~avg. 153RLU) vs. surface soil samples (~1,500-81,449RLU) [5]. However, the in-situ ATP assay failed in detecting presence of roots during the in-situ life detection experiment. Furthermore, cm-sized roots were overlooked during remote observations. Finally, ATP Luminometry provided insights for potential contamination from core-handling and environmental dust loadings on cleaned/sterilized control surfaces (e.g., 6,782-36,243RLU/cm2). Cleanliness/sterility can be maintained by applying a simple sterile protocol under field conditions. Science results from this research will support future Astrobiology driven drilling mission planned on Mars. Specifically, ground truth offers relevant insights to assess strengths and limits of in-situ/remote observations vs. laboratory measurements. Results from this experiment will also aid the debate on advantages/ disadvantages of manned vs. robotic drilling missions on Mars or other planets. [1] Boston et al., 1997; [2] http://marte.arc.nasa.gov; [3] Stoker, C., et al., 2006 AbSciCon, [4] Stoker et al., submitted; [5] Bonaccorsi., et al., 2006 AbSciCon.

Exploring the controls of soil biogeochemistry in a restored coastal wetland using object-oriented computer simulations of uptake kinetics and thermodynamic optimization in batch reactors

NASA Astrophysics Data System (ADS)

Payn, R. A.; Helton, A. M.; Poole, G.; Izurieta, C.; Bernhardt, E. S.; Burgin, A. J.

2012-12-01

Many hypotheses have been proposed to predict patterns of biogeochemical redox reactions based on the availability of electron donors and acceptors and the thermodynamic theory of chemistry. Our objective was to develop a computer model that would allow us to test various alternatives of these hypotheses against data gathered from soil slurry batch reactors, experimental soil perfusion cores, and in situ soil profile observations from the restored Timberlake Wetland in coastal North Carolina, USA. Software requirements to meet this objective included the ability to rapidly develop and compare different hypothetical formulations of kinetic and thermodynamic theory, and the ability to easily change the list of potential biogeochemical reactions used in the optimization scheme. For future work, we also required an object pattern that could easily be coupled with an existing soil hydrologic model. These requirements were met using Network Exchange Objects (NEO), our recently developed object-oriented distributed modeling framework that facilitates simulations of multiple interacting currencies moving through network-based systems. An initial implementation of the object pattern was developed in NEO based on maximizing growth of the microbial community from available dissolved organic carbon. We then used this implementation to build a modeling system for comparing results across multiple simulated batch reactors with varied initial solute concentrations, varied biogeochemical parameters, or varied optimization schemes. Among heterotrophic aerobic and anaerobic reactions, we have found that this model reasonably predicts the use of terminal electron acceptors in simulated batch reactors, where reactions with higher energy yields occur before reactions with lower energy yields. However, among the aerobic reactions, we have also found this model predicts dominance of chemoautotrophs (e.g., nitrifiers) when their electron donor (e.g., ammonium) is abundant, despite the fact that aerobic respiration produces a higher energy yield from the available dissolved oxygen. This suggests that incorporation of an alternative hypothesis, such as a maximum efficiency model, may be necessary to explain an observation of substantial aerobic respiration occurring in the presence of high ammonium and oxygen concentrations. We are parameterizing and testing this model based on results from batch reactor experiments that have treated soil slurries with a full factorial combination of various levels of reactive solutes found in freshwater (e.g., nitrate) and seawater (e.g., sulfate). Initial comparisons suggest that the model may need to account for the biogeochemical reactivity of iron and the potential physical influence of salt to properly describe variability in the biogeochemistry of Timberlake soils. Comparisons of these evolving models with field-derived data from soils will ultimately reveal how thermodynamic theory may be used to explain the evolution of nutrient retention and greenhouse gas emission in the Timberlake Wetland, where nutrient behavior is changing after restoration from agricultural land use and where inputs of brackish water are expected to increase due to sea level rise.

The Origin of Life in a Terrestrial Hydrothermal Pool? The Importance of a Catalytic Surface

NASA Astrophysics Data System (ADS)

Sydow, L. A.; Bennett, P.

2013-12-01

A premise of one chemoautotrophic theory for the origin of life is that a recurring reaction catalyzed on the charged surfaces of pyrite served as the first metabolism and was later enveloped by a primitive cellular membrane. This proposed 'surface metabolism' is analogous to the reductive acetyl-CoA pathway (Wächtershäuser 1988) and requires the abiotic formation of methanethiol (CH3SH), the simplest of the alkyl thiols, which would serve the role of coenzyme-A in the surface metabolism. Abiogenic CH3SH has not previously been identified in terrestrial hot springs, but it has been produced in the laboratory under hydrothermal conditions in the presence of a catalyst, usually FeS. Its formation would occur via the following reactions, with reaction 2 requiring catalysis: CO2 + 2H2S --> CS2 + 2H2O (1) CS2 + 3H2 --> CH3SH + H2S (2) We have identified CH3SH in Cinder Pool, an acid-sulfate-chloride hot spring in Yellowstone National Park. This spring is unusual in that it contains a subaqueous molten sulfur layer (~18 m depth) and thousands of iron-sulfur-spherules floating on the surface, which are created by gas bubbling through the molten floor of the spring. Analysis with EDS has shown that cinder material, largely composed of elemental sulfur, also contains trace iron sulfide minerals, meaning it could serve as a reactive and catalytic surface for abiogenic CH3SH formation in Cinder Pool. Furthermore, the cinders themselves are highly porous, and these void spaces could trap necessary reactants near the catalytic surface. Gas samples were collected from Cinder pool in fall of 2011 using the bubble strip method. One sample contained measurable quantities of CH3SH, and all samples contained related reactant sulfur gases such as large amounts of H2S, and smaller amounts of CS2 and dimethyl disulfide. Laboratory microcosm experiments were conducted to replicate these findings in a sterile environment to ensure CH3SH generation was abiotic. Analog Cinder Pool water and either FeS, FeS2, or cinders collected from the pool itself were incubated with H2, CO2, and CS2 as reaction gases for over a week at pool temperatures. An experiment was also conducted without CS2 to see if the solid materials could act as the sole source of sulfur. All of the experimental solids were capable of catalyzing CH3SH production when CS2 was added. Without added CS2, however, only cinders produced CH3SH, while FeS and FeS2 bottles could only make small amounts of H2S. Presumably, the large amount of elemental sulfur in the cinders creates enough H2S for the subsequent generation of CS2 then CH3SH, which is catalyzed by the trace iron-sulfide they also contain. Cinders act as an excellent reaction surface for CH3SH generation, and a similar material may have played a significant part in the advent of life on earth.

Biogeochemistry of Stinking Springs, Utah. Part II: Microbial Diversity and Photo- and Chemo-Autotrophic Growth Rates in a Layered Microbial Mat

NASA Astrophysics Data System (ADS)

Monteverde, D.; Metzger, J. G.; Bournod, C.; Kelly, H.; Johnson, H.; Sessions, A. L.; Osburn, M.; Shapiro, R. S.; Rideout, J.; Johnston, D. T.; Stevenson, B.; Stamps, B. W.; Vuono, D.; Hanselmann, K.; Spear, J. R.

2013-12-01

Layered microbial mats have garnered attention for their high phylogenetic diversity and exploitation of geochemical gradients often on the mm scale. However, despite their novelty and implications for early life diversification, little is known about layered microbial mat growth rates or the interdependence of the microbial communities within the system. Stinking Springs, a warm, sulfidic, saline spring northeast of the Great Salt Lake, serves as our test-site to investigate some of these questions. Stinking Springs undergoes downstream changes in pH (6.59-8.14), sulfide (527μM - below detection), sulfate (13-600μM), TCO2 (7.77-3.71mM), and temperature (40-21°C) along its ~150m flow path. The first 10m of discharge is channelized, beyond that, the spring supports a 10 to 40mm-thick layered microbial mat covering ~40% of the total spring runoff area. The mat was divided into four texturally-distinct layers which were each analyzed for 16S rRNA, lipid abundance, and bicarbonate and acetate uptake rates in addition to standard microscopy analyses. 16S rRNA analyses confirmed high taxa diversity within each layer, which varied significantly in taxa makeup such that no single phylum dominated the abundance (>33%) in more than one mat layer. The taxonomic diversity tended to increase with mat depth, a similar finding to other studies on layered microbial mats. A mat sampling transect across 16 meters showed that layer taxonomic diversity was conserved horizontally for all four mat layers, which implies mat depth has a larger control on diversity than physical or chemical parameters. Microscopy indicated the presence of diatoms in all layers which was confirmed by lipid abundance of sterols and long-branch fatty acid methyl esters. Incubation experiments were conducted in light and dark conditions over 24 hours with separate 13C-tagged bicarbonate and acetate additions. Heterotrophic growth rates (acetate uptake; 0.03-0.65%/day) were higher than autotrophic growth rates (bicarbonate uptake; 0-0.16%/day) under both dark and light conditions. Light conditions yielded higher growth rates for both heterotrophs and autotrophs and the highest rates were consistently found in the top mat layer and decreased with depth. The addition of 13C-acetate and concomitant high uptake is a measure of potential heterotrophy since in situ acetate concentrations are unlikely to be as high. 13C-bicarbonate uptake, on the other hand, should quantitatively represent the autotrophic growth rate. The Stinking Spring layered microbial mats display high taxonomic diversity, which is conserved horizontally across distances of meters and varies significantly with depth. Mats experience highest growth in the surface layer likely driven by phototrophs; high rates of bicarbonate uptake in the dark indicate considerable chemoautotrophy. Covariation in the heterotroph growth rates and 16S rRNA heterotroph abundance with mat depth indicates that heterotrophy may play an important role in the growth of these layered mats.

Cinder Pool's Sulfur Chemistry: Implications for the Origin of Life in Hydrothermal Environments

NASA Astrophysics Data System (ADS)

Sydow, L.; Bennett, P.; Nordstrom, D.

2012-12-01

One theory of the origin of life posits the abiotic formation of alkyl thiols as an initial step to forming biomolecules and eventually a simple chemoautotrophic cell. The premise of this theory is that a recurring reaction on the charged surfaces of pyrite served as a primordial metabolism analogous to the Acetyl-CoA pathway (Wächtershäuser 1988) and was later enveloped by a primitive cellular membrane. However, alkyl thiols have not previously been identified in terrestrial hot springs as unequivocally abiogenic. We have identified methanethiol (CH3SH), the simplest of the alkyl thiols, as well as dimethyl sulfide and dimethyldisulfide, in Cinder Pool, an acid-sulfate-chloride hot spring in the One Hundred Spring Plain of Norris Geyser Basin, Yellowstone National Park. It is unusual in that it contains a molten sulfur layer on the bottom (~20 m depth) and thousands of iron-sulfur-spherules floating on the surface (the iconic "cinders" the pool is named for), created by gas bubbling through the molten basement of the spring. These unique features make it a good candidate for abiotically generated CH3SH. Gas samples were collected from Cinder pool as well as an adjacent hydrothermal feature in the autumn of 2011 using the bubble strip method modified for use with hydrothermal waters. Several samples contained measurable quantities of methanethiol and other organic sulfur gases, with concentrations increasing with depth in the pool. Laboratory microcosm experiments were conducted to investigate the geochemical conditions required to abiotically form CH3SH. Sterile, artificial Cinder Pool water was injected into sterilized 60 mL serum bottles containing different iron-sulfur compounds, including cinders collected from the pool itself, as catalytic surfaces for the methanethiol-generating reaction. The bottles were then charged with hydrogen and carbon dioxide as reaction gases and incubated for a week at temperatures between 60 and 120oC. Bottles using FeS as a catalytic surface consistently produced methanethiol as expected from previous work. Bottles containing pyrite or cinders also generated lower but measurable quantities of CH3SH. While CH3SH is central to the autotroph-first theory and has been synthesized in the laboratory (e.g. Heinen and Lauwers 1996), it has not previously been observed to form abiotically in natural systems (although it is a common microbial byproduct of sulfur metabolism). We have identified CH3SH in a natural hydrothermal feature where it is unlikely to have formed secondary to microbial activity, as the only microorganism found in Cinder Pool is Aquificales Hydrogenobaculum (Spear et al. 2005) which can oxidize reduced sulfur compounds and would use methanethiol as a substrate, but should not form it as a byproduct. We have duplicated our field findings in sterile laboratory experiments using the cinders as a reactive surface. Also of note, the autotroph-first theory suggests that the primitive cellular membrane that enclosed the first metabolism was an FeS bubble created by a redox front (Russell and Hall 1997). While the cinders are not purely FeS, they could potentially serve this purpose based on the material's ability to function as a catalytic surface.

Preclinical molecular imaging: development of instrumentation for translational research with small laboratory animals.

PubMed

Mejia, Jorge; Miranda, Ana Claudia Camargo; Durante, Ana Claudia Ranucci; Oliveira, Larissa Rolim de; Barboza, Marycel Rosa Felisa Figols de; Rosell, Katerin Taboada; Jardim, Daniele Pereira; Campos, Alexandre Holthausen; Reis, Marilia Alves Dos; Catanoso, Marcela Forli; Galvis-Alonso, Orfa Yineth; Cabral, Francisco Romero

2016-01-01

To present the result of upgrading a clinical gamma-camera to be used to obtain in vivo tomographic images of small animal organs, and its application to register cardiac, renal and neurological images. An updated version of the miniSPECT upgrading device was built, which is composed of mechanical, electronic and software subsystems. The device was attached to a Discovery VH (General Electric Healthcare) gamma-camera, which was retired from the clinical service and installed at the Centro de Imagem Pré-Clínica of the Hospital Israelita Albert Einstein. The combined system was characterized, determining operational parameters, such as spatial resolution, magnification, maximum acceptable target size, number of projections, and acquisition and reconstruction times. Images were obtained with 0.5mm spatial resolution, with acquisition and reconstruction times between 30 and 45 minutes, using iterative reconstruction with 10 to 20 iterations and 4 projection subsets. The system was validated acquiring in vivo tomographic images of the heart, kidneys and brain of normal animals (mice and adult rats), using the radiopharmaceuticals technetium-labeled hexakis-2-methoxy-isobutyl isonitrile (99mTc-Sestamibi), technetium-labeled dimercaptosuccinic acid (99mTc-DMSA) and technetium-labeled hexamethyl propyleneamine oxime (99mTc-HMPAO). This kind of application, which consists in the adaptation for an alternative objective of already existing instrumentation, resulted in a low-cost infrastructure option, allowing to carry out large scale in vivo studies with enhanced quality in several areas, such as neurology, nephrology, cardiology, among others. Apresentar o resultado da adaptação de uma gama câmara clínica para uso dedicado na obtenção de imagens tomográficas in vivo de órgãos de pequenos animais de experimentação, e de sua aplicação na obtenção de imagens cardíacas, renais e neurológicas. Foi construída uma versão atualizada do dispositivo de adaptação miniSPECT, composto por três subsistemas: mecânico, eletrônico e de software. O dispositivo foi montado em uma câmara Discovery VH da General Electric Healthcare, retirada do serviço clínico e instalada no Centro de Imagem Pré-Clínica do Hospital Israelita Albert Einstein. O sistema combinado foi caracterizado, determinando parâmetros de funcionamento como resolução espacial, magnificação, limites de tamanho dos alvos de estudo, número de projeções, tempo de registro e tempo de reconstrução das imagens tomográficas. Foram obtidas imagens com resolução espacial de até 0,5mm, com tempos de registro e reconstrução de 30 a 45 minutos, utilizando reconstrução iterativa com 10 a 20 iterações e 4 subconjuntos de projeções. O sistema foi validado obtendo imagens tomográficas in vivo do coração, dos rins e do cérebro de animais normais (camundongos e ratos adultos), utilizando os radiofármacos hexaquis-2-metoxi-isobutil-isonitrila marcado com 99mTc (Sestamibi-99mTc), ácido dimercaptosuccínico marcado com 99mTc (DMSA-99mTc) e hexametil-propileno-amina-oxima marcada com 99mTc (HMPAO-99mTc). Este tipo de aplicação, que consiste na adaptação para um objetivo alternativo de instrumentação já existente, constituiu-se em uma opção de infraestrutura de baixo custo, que permite realizar estudos in vivo em larga escala, com qualidade aprimorada, em áreas diversas, como neurologia, nefrologia, cardiologia, entre outras.

DOE Office of Scientific and Technical Information (OSTI.GOV)

James C. Liao

This project is a collaboration with F. R. Tabita of Ohio State. Our major goal is to understand the factors and regulatory mechanisms that influence hydrogen production. The organisms to be utilized in this study, phototrophic microorganisms, in particular nonsulfur purple (NSP) bacteria, catalyze many significant processes including the assimilation of carbon dioxide into organic carbon, nitrogen fixation, sulfur oxidation, aromatic acid degradation, and hydrogen oxidation/evolution. Our part of the project was to develop a modeling technique to investigate the metabolic network in connection to hydrogen production and regulation. Organisms must balance the pathways that generate and consume reducing powermore » in order to maintain redox homeostasis to achieve growth. Maintaining this homeostasis in the nonsulfur purple photosynthetic bacteria is a complex feat with many avenues that can lead to balance, as these organisms possess versatile metabolic capabilities including anoxygenic photosynthesis, aerobic or anaerobic respiration, and fermentation. Growth is achieved by using H{sub 2} as an electron donor and CO{sub 2} as a carbon source during photoautotrophic and chemoautotrophic growth, where CO{sub 2} is fixed via the Calvin-Benson-Bassham (CBB) cycle. Photoheterotrophic growth can also occur when alternative organic carbon compounds are utilized as both the carbon source and electron donor. Regardless of the growth mode, excess reducing equivalents generated as a result of oxidative processes, must be transferred to terminal electron acceptors, thus insuring that redox homeostasis is maintained in the cell. Possible terminal acceptors include O{sub 2}, CO{sub 2}, organic carbon, or various oxyanions. Cells possess regulatory mechanisms to balance the activity of the pathways which supply energy, such as photosynthesis, and those that consume energy, such as CO{sub 2} assimilation or N{sub 2} fixation. The major route for CO{sub 2} assimilation is the CBB reductive pentose phosphate pathway, whose key enzyme is ribulose 1,5-biphosphate carboxylase/oxygenase (RubisCO). In addition to providing virtually all cellular carbon during autotrophic metabolism, RubisCO-mediated CO{sub 2} assimilation is also very important for nonsulfur purple photosynthetic bacteria under photoheterotrophic growth conditions since CO{sub 2} becomes the major electron sink under these conditions. In this work, Ensemble Modeling (EM) was developed to examine the behavior of CBB-compromised RubisCO knockout mutant strains of the nonsulfur purple photosynthetic bacterium Rhodobacter sphaeroides. Mathematical models of metabolism can be a great aid in studying the effects of large perturbations to the system, such as the inactivation of RubisCO. Due to the complex and highly-interconnected nature of these networks, it is not a trivial process to understand what the effect of perturbations to the metabolic network will be, or vice versa, what enzymatic perturbations are necessary to yield a desired effect. Flux distribution is controlled by multiple enzymes in the network, often indirectly linked to the pathways of interest. Further, depending on the state of the cell and the environmental conditions, the effect of a perturbation may center around how it effects the carbon flow in the network, the balancing of cofactors, or both. Thus, it is desirable to develop mathematical models to describe, understand, and predict network behavior. Through the development of such models, one may gain the ability to generate a set of testable hypotheses for system behavior.« less

Quantifying microbial activity in deep subsurface sediments using a tritium based hydrognease enzyme assay

NASA Astrophysics Data System (ADS)

Adhikari, R.; Nickel, J.; Kallmeyer, J.

2012-12-01

Microbial life is widespread in Earth's subsurface and estimated to represent a significant fraction of Earth's total living biomass. However, very little is known about subsurface microbial activity and its fundamental role in biogeochemical cycles of carbon and other biologically important elements. Hydrogen is one of the most important elements in subsurface anaerobic microbial metabolism. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways. They either consume or produce protons for ATP synthesis. Hydrogenase (H2ase) is a ubiquitous intracellular enzyme that catalyzes the interconversion of molecular hydrogen and/or water into protons and electrons. The protons are used for the synthesis of ATP, thereby coupling energy generating metabolic processes to electron acceptors such as CO2 or sulfate. H2ase enzyme targets a key metabolic compound in cellular metabolism therefore the assay can be used as a measure for total microbial activity without the need to identify any specific metabolic process. Using the highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey, in marine sediments of the Barents Sea and in deep subseafloor sediments from the Nankai Trough. H2ase activity could be quantified at all depths of all sites but the activity distribution varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from ca. 20 mmol H2 cm-3d-1 close to the sediment-water interface to 0.5 mmol H2 cm-3d-1 at a depth of 0.8 m. In samples from the Barents Sea H2ase activity ranged between 0.1 to 2.5 mmol H2 cm-3d-1 down to a depth of 1.60 m. At all sites the sulfate reduction rate profile followed the upper part of the H2ase activity profile until sulfate reduction reached the minimum detection limit (ca. 10 pmol cm-3d-1). H2ase activity could still be quantified after the decline of sulfate reduction, indicating that other microbial processes are becoming quantitatively more important. Similarly, H2ase activity could be quantified at greater depths (ca. 400 mbsf) in Nankai Trough sediments. Nankai Trough is one of the world's most geologically active accretionary wedges, where the Philippine Plate is subducting under the southwest of Japan. Due to the transient faulting, huge amounts of energy are liberated that enhance chemical transformations of organic and inorganic matter. An increase in H2ase activity could be observed at greater depth, which suggests that microbial activity is stimulated by the fault activity. Current techniques for the quantification of microbial activity in deep sediments have already reached their physical and technical limits and-in many cases- are still not sensitive enough to quantify extremely low rates of microbial activity. Additional to the quantification of specific processes, estimates of total microbial activity will provide valuable information on energy flux and microbial metabolism in the subsurface biosphere and other low-energy environments as well as help identifying hotspots of microbial activity. The tritium H2ase assay has a potential to become a valuable tool to measure total subsurface microbial activity.

Biomineralization and biosignatures of coralloid-type speleothems from lava tubes of Galapagos Islands: evidences on the fossil record of prokaryotes

NASA Astrophysics Data System (ADS)

Miller, Ana Z.; Garcia-Sanchez, Angela M.; Pereira, Manuel F. C.; Gazquez, Fernando; Calaforra, José M.; Forti, Paolo; Toulkeridis, Theofilos; Martínez-Frías, Jesús; Saiz-Jimenez, Cesareo

2016-04-01

Lava tubes have traditionally been considered of little interest from a mineralogical point of view. Recently, this type of volcanic caves has received particular attention because lava tubes have been described on Mars. Speleothems, or secondary mineral deposits in lava tubes are mainly composed of siliceous minerals. Coralloid-type speleothems are found either on basaltic cave walls or on the surface of other speleothems. Several authors attribute a microbially mediated origin to their formation. This type of speleothems was recorded within Royal Palm Cave of Santa Cruz Island in Galapagos Archipelago (Ecuador), a lava tube 600 m long, 5 to 15 m height and 2 to 10 m width. The Galapagos Islands are an archipelago of 19 volcanic islands located some 1500 km west of Ecuador, in the Pacific Ocean. These islands host one of the most biodiverse settings on Earth, studied by Charles Darwin. Beige and greyish small coralloids were collected in Royal Palm Cave and analysed by field emission scanning electron microscopy with energy dispersive X-ray spectroscopy (FESEM-EDS), X-ray micro-computed tomography (micro-CT) and mineralogical analyses for morphological, 3D microstructural and compositional characterization, as well as for assessing microbe-mineral interactions and biogenicity. In addition, 16S rRNA gene analyses were performed to identify microbial communities associated with the coralloid-type speleothems. The coralloids showed internal compositional zonation along the growth direction of the speleothems, according to micro-CT data. Internal layering was clearly discernable by the differences in opacity of the distinct mineralogical phases to X-rays, being dominated by alteration products of siliceous composition, whereas more opaque phases, usually Ca-rich minerals, were dominant in the outermost part of the speleothems. X-ray diffraction and infrared spectroscopy reinforced that the first stage of deposition is mainly composed of opal A and clay minerals, whereas the final stage mainly consists of low crystalline calcite. FESEM-EDS analysis revealed mineralized bacterial filaments rich in Si on the coralloid samples, as well as minerals precipitation associated with extracellular polymeric substances (EPS), which serve as nuclei for preferential precipitation on the extracellular sheaths. This suggests that biological activity played a major role in the development of these speleothems. In addition, imprints of filamentous cells and microboring readily preserved on siliceous minerals were observed on the coralloid speleothems. These features are recognized as biosignatures valuable for astrobiology and may represent modern analogs of the fossil record of prokaryotes. DNA-based analyses showed that bacteria belonging to Actinobacteria (31%) Gemmatimonadetes (25%) and Proteobacteria (24%) phyla dominated in this cave ecosystem, followed by Acidobacteria, Firmicutes and Nitrospirae. Most of the identified phylotypes were affiliated to chemoautotrophs, including thermophilic bacteria such as Ferrithrix thermotolerans, and other mineral utilizing microorganisms like Aciditerrimonas ferrireducens, Desulfuromonas sp. and Desulfovibrio sp., indicating that Galapagos lava tubes host highly specialized subsurface biosphere dominated by microorganisms able to interact with minerals and promote biomineralization. Acknowledgments: This work has been supported by the project PC-65-14 from the Ministry of Environment of Ecuador. AZM acknowledges the support from the Marie Curie Fellowship of the 7th EC Framework Programme (PIEF-GA-2012-328689-DECAVE). The authors acknowledge the Spanish Ministry of Economy and Competitiveness (project CGL2013-41674-P) and FEDER funds for financial support.

Harpacticoid copepods-their symbiotic associations and biogenic substrata: a review.

PubMed

Huys, Rony

2016-10-11

Members of the order Harpacticoida are primarily free-living and benthic but some lineages have adopted alternative modes of life which involve a major habitat shift or dependence on a host. Since the first discovery of a harpacticoid associated with an invertebrate host about 150 years ago, a total of 172 species, representing 84 genera and 17 families, have been shown to live in symbiotic partnership with other organisms. The steady addition of new taxa during the last 35 years testifies to the widespread and previously underestimated occurrence of symbiosis in the group. Harpacticoids have entered into associations with Cyanobacteria, Protozoa, macroalgae, grasses, fish hosts, marine tetrapods (including whales, sea turtles and manatees) and at least eleven invertebrate phyla. At present, 86 independent colonizations of marine and freshwater host organisms can be identified but this number is a minimum estimate and is expected to increase as certain host groups will be more properly sampled. In contrast to the Cyclopoida and Siphonostomatoida, which have been extremely successful in developing associations with cnidarians, sponges, echinoderms and ascidiaceans, members of the Harpacticoida have a marked predilection for crustacean hosts. Except for a few species that can be classified as genuine parasites, the precise nature of the relationship between most associated harpacticoids and their hosts has yet to be elucidated but can probably be defined as commensalistic, where the benefit to the copepod may be nutritional or protective. Most are ectosymbiotic but some live as endocommensals in microhabitats which provide considerable protection from predation. The success of symbiotic harpacticoids in freshwater is limited with the few species known to be associated with freshwater hosts typically representing isolated forays into a symbiotic lifestyle from an otherwise free-living lineage. The scattered literature on symbiotic harpacticoids is compiled and presented by host group. Dichotomous keys are provided for the identification of most species while accidental and doubtful records are discussed where appropriate.The genus Idomenella T. Scott, 1906a (Pseudotachidiidae), previously a junior subjective synonym of Dactylopodella Sars, 1905a, is reinstated to accommodate Dactylopodella rostrata (T. Scott, 1893), D. janetae Hicks, 1989, Xouthous coronatus (T. Scott, 1894b), X. antarcticus (Giesbrecht, 1902), X. intermedius (Lang, 1934) and Idomenella paracoronata sp. nov. Kioloaria Harris, 1994 (Porcellidiidae) is adopted as the valid replacement name for the preoccupied Acutiramus Harris, 2014a. The name of a second porcellidiid genus, Murramia Harris, 1994, lacks the mandatory type fixation and is made available here by adopting the original name but taking the present authorship and date. The generic name Ellucana Sewell, 1940 is currently unavailable and must instead be attributed to Coull (1971b). Laophonte commensalis Raibaut, 1962a is fixed as the type of Raibautius gen. nov. in the family Laophontidae, Tegastes cnidicus Humes, 1981b as the type of Aglaogastes gen. nov. in the Tegastidae, and Canuella (Canuella) indica Krishnaswamy, 1957 as the type of Indicanuella gen. nov.A number of new names are proposed for species that had previously been misidentified: Diarthrodes septemtrionalis sp. nov. for D. roscoffensis (Monard, 1935b) sensu Kornev & Chertoprud (2008), Kioloaria jejuensis sp. nov. for Porcellidium brevicaudatum Thompson & Scott, 1903 sensu Kim & Kim (1996), Xouthous andamanensis sp. nov. for X. maldivae [sic] Sewell, 1940 sensu Wells & Rao (1987), X. wellsi sp. nov. for X. laticaudatus (Thompson & Scott, 1903) sensu Wells (1967), X. namibiensis sp. nov. for X. pectinatus (Scott & Scott, 1898) sensu Kunz (1963), and Idomenella paracoronata sp. nov. for Idomene coronata (T. Scott, 1894b) sensu Sars (1909a). The inadequately described Amenophia ovalis Brady, 1910 is relegated to a species inquirenda in Amenophia Boeck, 1865. Idomene australis Brady, 1910, I. pusilla Brady, 1910, Dactylopusia ferrieri T. Scott, 1912 and I. kabylica Monard, 1936 are ranked species incertae sedis in the Pseudotachidiidae. Dactylopus bahamensis Edwards, 1891 is tentatively considered as species incertae sedis in the Dactylopusiidae. Canuellina onchophora Por, 1967 and C. nicobaris Wells & Rao, 1987 are transferred to the genus Ellucana Coull, 1971b while Ellucana secunda Coull, 1971b is assigned to the genus Canuellina Gurney, 1927. Xylora calyptogenae Willen, 2006 is sunk as a junior subjective synonym of X. bathyalis Hicks, 1988a. The incorrect original spellings of Parathalestris pacificus Chislenko, 1971, P. infestus Ho & Hong, 1988, Tripartisoma ovalis Avdeev, 1983, T. trapezoidalis Avdeev, 1983, Amplipedicola pectinatus Avdeev, 2010 and Sunaristes japonicus Ho, 1986a are amended to reflect agreement in gender with their respective generic names.

A lander mission to probe subglacial water on Saturn's moon Enceladus for life

NASA Astrophysics Data System (ADS)

Konstantinidis, Konstantinos; Flores Martinez, Claudio L.; Dachwald, Bernd; Ohndorf, Andreas; Dykta, Paul; Bowitz, Pascal; Rudolph, Martin; Digel, Ilya; Kowalski, Julia; Voigt, Konstantin; Förstner, Roger

2015-01-01

The plumes discovered by the Cassini mission emanating from the south pole of Saturn's moon Enceladus and the unique chemistry found in them have fueled speculations that Enceladus may harbor life. The presumed aquiferous fractures from which the plumes emanate would make a prime target in the search for extraterrestrial life and would be more easily accessible than the moon's subglacial ocean. A lander mission that is equipped with a subsurface maneuverable ice melting probe will be most suitable to assess the existence of life on Enceladus. A lander would have to land at a safe distance away from a plume source and melt its way to the inner wall of the fracture to analyze the plume subsurface liquids before potential biosignatures are degraded or destroyed by exposure to the vacuum of space. A possible approach for the in situ detection of biosignatures in such samples can be based on the hypothesis of universal evolutionary convergence, meaning that the independent and repeated emergence of life and certain adaptive traits is wide-spread throughout the cosmos. We thus present a hypothetical evolutionary trajectory leading towards the emergence of methanogenic chemoautotrophic microorganisms as the baseline for putative biological complexity on Enceladus. To detect their presence, several instruments are proposed that may be taken aboard a future subglacial melting probe. The "Enceladus Explorer" (EnEx) project funded by the German Space Administration (DLR), aims to develop a terrestrial navigation system for a subglacial research probe and eventually test it under realistic conditions in Antarctica using the EnEx-IceMole, a novel maneuverable subsurface ice melting probe for clean sampling and in situ analysis of ice and subglacial liquids. As part of the EnEx project, an initial concept study is foreseen for a lander mission to Enceladus to deploy the IceMole near one of the active water plumes on the moon's South-Polar Terrain, where it will search for signatures of life. The general mission concept is to place the Lander at a safe distance from an active plume. The IceMole would then be deployed to melt its way through the ice crust to an aquiferous fracture at a depth of 100 m or more for an in situ examination for the presence of microorganisms. The driving requirement for the mission is the high energy demand by the IceMole to melt through the cold Enceladan ices. This requirement is met by a nuclear reactor providing 5 kW of electrical power. The nuclear reactor and the IceMole are placed on a pallet lander platform. An Orbiter element is also foreseen, with the main function of acting as a communications relay between Lander and Earth. After launch, the Lander and Orbiter will perform the interplanetary transfer to Saturn together, using the on-board nuclear reactor to power electric thrusters. After Saturn orbit insertion, the Combined Spacecraft will continue using Nuclear Electric Propulsion to reach the orbit of Enceladus. After orbit insertion at Enceladus, the Orbiter will perform a detailed reconnaissance of the South-Polar Terrain. At the end of the reconnaissance phase, the Lander will separate from the Orbiter and an autonomously guided landing sequence will place it near one of the active vapor plumes. Once landed, the IceMole will be deployed and start melting through the ice, while navigating around hazards and towards a target subglacial aquiferous fracture. An initial estimation of the mission's cost is given, as well as recommendations on the further development of enabling technologies. The planetary protection challenges posed by such a mission are also addressed.

Development of biological platform for the autotrophic production of biofuels

NASA Astrophysics Data System (ADS)

Khan, Nymul

The research described herein is aimed at developing an advanced biofuel platform that has the potential to surpass the natural rate of solar energy capture and CO2 fixation. The underlying concept is to use the electricity from a renewable source, such as wind or solar, to capture CO 2 via a biological agent, such as a microbe, into liquid fuels that can be used for the transportation sector. In addition to being renewable, the higher rate of energy capture by photovoltaic cells than natural photosynthesis is expected to facilitate higher rate of liquid fuel production than traditional biofuel processes. The envisioned platform is part of ARPA-E's (Advanced Research Projects Agency - Energy) Electrofuels initiative which aims at supplementing the country's petroleum based fuel production with renewable liquid fuels that can integrate easily with the existing refining and distribution infrastructure (http://arpae. energy.gov/ProgramsProjects/Electrofuels.aspx). The Electrofuels initiative aimed to develop liquid biofuels that avoid the issues encountered in the current generation of biofuels: (1) the reliance of biomass-derived technologies on the inefficient process of photosynthesis, (2) the relatively energy- and resource-intensive nature of agronomic processes, and (3) the occupation of large areas of arable land for feedstock production. The process proceeds by the capture of solar energy into electrical energy via photovoltaic cells, using the generated electricity to split water into molecular hydrogen (H2) and oxygen (O2), and feeding these gases, along with carbon dioxide (CO2) emitted from point sources such as a biomass or coal-fired power plant, to a microbial bioprocessing platform. The proposed microbial bioprocessing platform leverages a chemolithoautotrophic microorganism (Rhodobacter capsulatus or Ralstonia eutropha) naturally able to utilize these gases as growth substrates, and genetically modified to produce a triterpene hydrocarbon fuel molecule (C30+ botryococcenes) native to the alga Botryococcus braunii . In addition to the genetic modification and bioreactor performance studies of these organisms for the production of botryococcene or squalene, the research examined the potential economic feasibility of the proposed platform through the use of bioreactor, microbial energetic models and experimentally measured growth yield and maintenance coefficients. In order to carry out an economic analysis, a process model was created in Aspen with the bioreactor at the center. This is presented in Chapter 2. The model looked at the effects of growth yield and maintenance coefficients of R. capsulatus and R. eutropha, reactor residence time, gas-liquid mass-transfer coefficients, gas composition and specific fuel productivity on the volumetric productivity and fuel yield on H2. It was found that the organism with the lowest maintenance coefficient performed better under very low growth rates evaluated in the model (based on residence time through the reactor) performed the best. The optimum parameter values were then used to determine the capital and operating costs for a 5000 bbl-fuel/day plant and the final fuel cost based on the Levelized Cost of Electricity (LCOE). It was found that under the assumptions used in this analysis and crude oil prices, the LCOE required for economic feasibility must be less than 2¢/kWh. While not feasible under current market prices and costs, this work identifies key variables impacting process cost and discusses potential alternative paths toward economic feasibility. This was the best case scenario of the two organisms evaluated, and an optimally suited organism with high growth yield and low maintenance coefficient should obviously improve the economics. This economic constraint will improve with the rise of fossil fuel prices, which should occur if the environmentally detrimental effects of their use are factored into the price, through higher taxation, for example. A review of the current status of metabolic engineering of chemolithoautotrophs is carried out in order to identify the challenges and likely routes to overcome them. This is presented in Chapter 3 of this dissertation. The initial metabolic engineering and bioreactor studies was carried out using a number of gene-constructs on R. capsulatus and R. eutropha. The gene-constructs consisted of Plac promoter followed by the triterpene synthase genes (SS or BS) and other upstream genes. A comparison of the production of triterpenes were done in the different growth modes that R. capsulatus was capable of growing---aerobic heterotrophic, anaerobic photoheterotrophic and aerobic chemoautotrophic. Autotrophic productivity could likely be improved much further by increasing the available mass-transfer of the reactor. These efforts are presented in Chapter 4 of this dissertation. (Abstract shortened by UMI.).

Worldwide Eutrophication of Water Bodies: Causes, Concerns, Controls

NASA Astrophysics Data System (ADS)

Prepas, E. E.; Charette, T.

2003-12-01

Eutrophication is the nutrient enrichment of waters that stimulates an array of symptomatic changes, that can include increased phytoplankton and rooted aquatic plant (macrophyte) production, fisheries and water quality deterioration, and other undesirable changes that interfere with water uses (Bartsch, 1972). The trophic state, or degree of fertility, of water bodies ranges from oligotrophic to mesotrophic to eutrophic with increasing supply of nutrients and organic matter ( Table 1). Eutrophication is most often the result of an elevated supply of nutrients, particularly nitrogen and phosphorus, to surface waters that results in enhanced production of primary producers, particularly phytoplankton and aquatic plants. Table 1. Mean annual values for the trophic classification system Total phosphorus (μg L-1)Chlorophyll a (μg L-1)Secchi disk depth (m) Ultra-oligotrophic<4<1>12 Oligotrophic<10<2.5>6 Mesotrophic10-352.5-86-3 Eutrophic35-1008-253-1.5 Hypertrophic>100>25<1.5 Source: OECD (1982). Phytoplankton are unpleasant at high densities. The sight and smell of clots or masses of decaying phytoplankton decreases the recreational value of most waters and usually generates concerns among the public. Furthermore, blooms of toxin-producing phytoplankton can cause widespread illness. A bloom is a conspicuous concentration of phytoplankton, often concentrated at or near the surface. It is difficult to quantify what constitutes a "bloom," but a rough estimate places it as a chlorophyll a concentration over 30 μg L-1. Toxins produced by dinoflagellates such as Pfiesteria in marine environments of the northeastern US and red tides in tropical waters have caused massive fish kills, millions of dollars in losses to seafood-related industries, human memory loss, paralysis, and even death (Van den Hoeck et al., 1995; Silbergeld et al., 2000). Bloom-forming species of cyanobacteria can produce potent hepato-(liver) toxins termed microcystins that have been implicated in poisonings of domestic livestock, pets, wildlife, and susceptible humans ( Codd, 1995; Dunn, 1996). In addition, an accumulation of dead phytoplankton in bottom waters of eutrophic systems can lead to high decomposition rates by bacteria. Dissolved oxygen consumption by decomposers, combined with a barrier to gas exchange (thermocline or ice cover), can reduce (hypoxia) or eliminate (anoxia) dissolved oxygen in bottom waters. (A thermocline is the junction between an upper layer of warm, less dense water (the epilimnion) and a deeper layer of cold water (the hypolimnion). When this stratification is in place, the typically oxygen-rich waters of the epilimnion do not mix with the waters of the hypolimnion.) Oxygen depletion is one of the most harmful side effects of eutrophication because it can cause catastrophic fish kills, devastating local fisheries.The accumulation of plant biomass depends on the addition of factors that stimulate plant growth. On average, the macronutrients nitrogen and phosphorus are present in marine phytoplankton at an atomic ratio 16 : 1 (Redfield, 1958). The ratio of nitrogen to phosphorus in freshwaters tends to be greater than the ratio in phytoplankton; therefore, phosphorus most often limits the growth of phytoplankton. As a result, phosphorus enrichment of freshwater often causes its eutrophication ( Schindler, 1977). In lakes, nitrogen is usually present in concentrations equal to or beyond what is required for aquatic plant growth because, unlike phosphorus, it has an atmospheric source. In marine systems, nitrogen concentrations are often limiting because bacterial nitrogen fixation, while a considerable source of nitrogen in lakes, not as important in marine waters. A wide variety of prokaryotic organisms (i.e., certain cyanobacteria, heterotrophic, and chemoautotrophic bacteria) can use nitrogen gas directly and incorporate it into organic compounds through a process called nitrogen fixation. Nitrogen fixation is an enzyme-catalyzed process that reduces nitrogen gas (N2) to ammonia (NH3). Nitrogen-fixing cyanobacteria make up less than 1% of the total biomass of phytoplankton in estuaries of the Atlantic coast of North America, whereas in lakes they often make up more than 50% of phytoplankton biomass (reviewed in Howarth, 1988). An increase in water clarity can also spur the growth of aquatic vegetation in systems where the clarity of water is poor from high concentrations of suspended particles.The biodiversity of most aquatic systems decreases with eutrophication (Figure 1). Phytoplankton species diversity is reduced in highly productive systems. Cyanobacteria are usually dominant in eutrophic systems because these organisms are better adapted to conditions of high nutrients (Smith, 1986; Trimbee and Prepas, 1987; Watson et al., 1997). In addition, fish and macro-invertebrate species diversity can decrease with eutrophication. Depletion of dissolved oxygen in deep water is associated with eutrophication and can lead to a loss or displacement of species intolerant of such conditions ( Ludsin et al., 2001). In eutrophic lakes of North America, characteristic fish types are surface-dwelling, warm water fishes such as pike, perch, and bass, as compared to deep-dwelling, cold-water fishes like salmon, trout, and cisco ( Ryding and Rast, 1989). (9K)Figure 1. Suggested changes in various characteristics of lakes with eutrophication (reproduced by permission of Cambridge University Press from Welch, E. B., Ecological Effects of Waste Water, 1980, p. 273).