The effect of microorganisms and seasonal factors on the isotopic composition of particulate organic carbon from the black sea

The isotopic composition of particulate organic carbon (POC) from the Black Sea deep-water zone was studied during a Russian-Swiss expedition in May 1998. POC from the upper part of the hydrogen sulfide zone (the C-layer) was found to be considerably enriched with the¹²C isotope, as compared to the POC of the oxycline and anaerobic zone. In the C-layer waters, the concurrent presence of dissolved oxygen and hydrogen sulfide and an increased rate of dark CO₂ fixation were recorded, suggesting that the change in the POC isotopic composition occurs at the expense of newly formed isotopically light organic matter of the biomass of autotrophic bacteria involved in the sulfur cycle. In the anaerobic waters below the C-layer, the organic matter of the biomass of autotrophs is consumed by the community of heterotrophic microorganisms; this results in weighting of the POC isotopic composition. Analysis of the data obtained and data available in the literature allows an inference to be made about the considerable seasonable variability of the POC δ¹³C value, which depends on the ratio of terrigenic and planktonogenic components in the particulate organic matter.     

The “Cycle of Life” in Ecology: Sergei Vinogradskii’s Soil Microbiology, 1885–1940

Historians of science have attributed the emergence of ecology as a discipline in the late nineteenth century to the synthesis of Humboldtian botanical geography and Darwinian evolution. In this essay, I begin to explore another, largely neglected but very important dimension of this history. Using Sergei Vinogradskii’s career and scientific research trajectory as a point of entry, I illustrate the manner in which microbiologists, chemists, botanists, and plant physiologists inscribed the concept of a “cycle of life” into their investigations. Their research transformed a longstanding notion into the fundamental approaches and concepts that underlay the new ecological disciplines that emerged in the 1920s. Pasteur thus joins Humboldt as a foundational figure in ecological thinking, and the broader picture that emerges of the history of ecology explains some otherwise puzzling features of that discipline – such as its fusion of experimental and natural historical methodologies. Vinogradskii’s personal “cycle of life” is also interesting as an example of the interplay between Russian and Western European scientific networks and intellectual traditions. Trained in Russia to investigate nature as a super-organism comprised of circulating energy, matter, and life; over the course of five decades – in contact with scientists and scientific discourses in France, Germany, and Switzerland – he developed a series of research methods that translated the concept of a “cycle of life” into an ecologically conceived soil science and microbiology in the 1920s and 1930s. These methods, bolstered by his authority as a founding father of microbiology, captured the attention of an international network of scientists. Vinogradskii’s conceptualization of the “cycle of life” as chemosynthesis, autotrophy, and global nutrient cycles attracted the attention of ecosystem ecologists; and his methods appealed to practitioners at agricultural experiment stations and microbiological institutes in the United States, Western Europe, and the Soviet Union.     

Microbial processes at the Lost City vent field,Mid-Atlantic Ridge

Microbiological and biogeochemical measurements showed that the intensities of CO₂ assimilation, methane oxidation, and sulfate reduction at the Lost City vent field (3° N) reach 3.8 µg C/(1 day), 0.06 µg C/(1 day), and 117 µg S/(1 day), respectively. On the surface of the carbonate structures occurring at this field, two varieties of bacterial mats were found. The first variety, which is specific to the Lost City alkaline vent field, represents jellylike bacterial mats dominated by slime-producing bacteria of several morphotypes. This mat variety also contains chemolithotrophic and heterotrophic microorganisms, either microaerobic or anaerobic. The intensities of CO₂ assimilation, methane oxidation, and sulfate reduction in this variety reach 747 µg C/(dm³ day), 0.02 µg C/(dm³ day), and 28000 µg S/(dm³ day), respectively. Bacterial mats of the second variety are formed by nonpigmented filamentous sulfur bacteria, which are close morphologically to Thiothrix. The intensities of CO₂ assimilation, methane oxidation, and sulfate reduction in the second mat variety reach 8.2 µg C/(dm³ day), 5.8 µg C/(dm³ day), and 17000 µg S/(dm³ day), respectively. These data suggest the existence of subsurface microflora at the Lost City vent field.Translated from Mikrobiologiya, Vol. 74, No. 1, 2005, pp. 111–118.Original Russian Text Copyright © 2005 by Dulov, Lein, Dubinina, Pimenov.     

Provannid and provannid‐like gastropods from the Late Cretaceous cold seeps of Hokkaido (Japan) and the fossil record of the Provannidae (Gastropoda: Abyssochrysoidea)

A fauna of provannid and provannid‐like shells is described from Upper Cretaceous seep carbonates in Hokkaido, Japan. We describe two new provannid species, Provanna tappuensis sp. nov. and Desbruyeresia kanajirisawensis sp. nov. , with preserved protoconchs of unquestionable provannid type with decollate apex. This material confirms the occurrence of Provannidae as early as the Middle Cenomanian. We also describe Hokkaidoconcha gen. nov. and a new family Hokkaidoconchidae fam. nov. , with two named species, H. hikidai sp. nov. and H. tanabei sp. nov . Hokkaidoconchidae are possibly related to the Provannidae, judging from a similar, but not decollate larval shell, although the juvenile teleoconch whorls differ in being of a general cerithimorph appearance and the details of the aperture are unknown. Furthermore, we review the published fossil record of Provannidae and Abyssochrysidae, and we consider that in those older than the Eocene, there is no evidence preserved that unequivocally supports a position there. The Jurassic Acanthostrophia acanthica from Italy seems to be the oldest known record of Abyssochrysidae, and the most reliable occurrence of the family, older than from the Miocene. Other fossil, pre‐Miocene species that have been classified in the Abyssochryssidae are provisionally referred to Hokkaidoconchidae. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154 , 421–436.     

Widespread methanotrophic primary production in lowland chalk rivers

Methane is oversaturated relative to the atmosphere in many rivers, yet its cycling and fate is poorly understood. While photosynthesis is the dominant source of autotrophic carbon to rivers, chemosynthesis and particularly methane oxidation could provide alternative sources of primary production where the riverbed is heavily shaded or at depth beneath the sediment surface. Here, we highlight geographically widespread methanotrophic carbon fixation within the gravel riverbeds of over 30 chalk rivers. In 15 of these, the potential for methane oxidation (methanotrophy) was also compared with photosynthesis. In addition, we performed detailed concurrent measurements of photosynthesis and methanotrophy in one large chalk river over a complete annual cycle, where we found methanotrophy to be active to at least 15 cm into the riverbed and to be strongly substrate limited. The seasonal trend in methanotrophic activity reflected that of the riverine methane concentrations, and thus the highest rates were measured in mid-summer. At the sediment surface, photosynthesis was limited by light for most of the year with heavy shading induced by dense beds of aquatic macrophytes. Across 15 rivers, in late summer, we conservatively calculated that net methanotrophy was equivalent to between 1% and 46% of benthic net photosynthetic production within the gravel riverbed, with a median value of 4%. Hence, riverbed chemosynthesis, coupled to the oxidation of methane, is widespread and significant in English chalk rivers.     

Exploration of a Submerged Sinkhole Ecosystem in Lake Huron

Dissolution of the Silurian-Devonian aquifer in the Lake Huron Basin has produced several karst formations in the bedrock (sinkholes), through which groundwater emerges onto the lake floor. During September 2003, we explored a recently discovered submerged sinkhole ecosystem (55 m × 40 m × ∼1 m) located at a depth of 93 m with a remotely operated vehicle (ROV) equipped with a conductivity-temperature-depth (CTD) system, an acoustic navigational system, a video camera, and a water sampling system. In addition to two morphotypes of benthic mats, a 1–2 m thick visibly cloudy near-bottom nepheloid-like layer (sinkhole plume) with a strong hydrogen sulfide odor prevailed just above the seepage area of clear water. Relative to lake water, water samples collected within the sinkhole plume were characterized by slightly higher (by 4°C) temperatures, very high levels of chloride (up to 175 mg l⁻¹) and conductivity (1,700 μS cm⁻¹), as well as extremely high concentrations of sulfate (1,400 mg l⁻¹), phosphorus (3 mg l⁻¹) and particulate organic matter (400 mg C l⁻¹). Compared to background lake water, sinkhole plume water was characterized by approximately twofold lower C:N ratios and tenfold higher levels of dissolved organic carbon, bacterial biomass as well as heterotrophic bacterial production. Significant uptake of ¹⁴C-bicarbonate in dark incubations provided preliminary evidence for occurrence of chemosynthesis, possibly mediated by specialized Bacteria and Archea present in this submerged sinkhole ecosystem in the Laurentian Great Lakes.     

The Role of Microbes in Agriculture: Sergei Vinogradskii’s Discovery and Investigation of Chemosynthesis, 1880–1910

In 1890, Sergei Nikolaevich Vinogradskii (Winogradsky) proposed a novel life process called chemosynthesis. His discovery that some microbes could live solely on inorganic matter emerged during his physiological research in 1880s in Strassburg and Zurich on sulfur, iron, and nitrogen bacteria. In his nitrification research, Vinogradskii first embraced the idea that microbiology could have great bearing on agricultural problems. His critique of agricultural chemists and Kochian-style bacteriologists brought this message to the broader agricultural community, resulting in an heightened interest in biological, rather than chemical methods to investigate soil processes. From 1891 to 1910, he directed the microbiological laboratory at the Imperial Institute of Experimental Medicine in St. Petersburg, Russia, where he expanded his chemosynthesis research to a broad investigation of the manifold significance of autotrophic organisms in soil processes. This work and that of his students attracted the serious attention of agricultural chemists and soil scientists in Russia and abroad, changing essentially the way they understood and investigated the role of microbes in the soil. His student, Vasilii Omelianskii, effectively integrated Vinogradskii’s approach into Russian and Soviet, and international agricultural microbiology. Vinogradskii’s activities in the late 19th century reflect the changes occurring more broadly in science. At that time, microbiologists such as Louis Pasteur, Eugenius Warming, and Martianus Beijerinck were contributing new laboratory methods and theoretical perspectives to incipient disciplines closely related to agriculture: ecology, soil science, and soil microbiology.     

Neutrophilic Iron-Oxidizing Bacteria in the Ocean: Their Habitats,Diversity, and Roles in Mineral Deposition,Rock Alteration,and Biomass Production in the Deep-Sea

The importance of metals to life has long been appreciated. Iron (Fe) is the fourth most abundant element overall, and the second most abundant element that is redox-active in near-surface aqueous habitats, rendering it the most important environmental metal. While it has long been recognized that microorganisms participate in the global iron cycle, appreciation for the pivotal role that redox cycling of iron plays in energy conservation among diverse prokaryotes has grown substantially in the past decade. In addition, redox reactions involving Fe are linked to several other biogeochemical cycles (e.g., carbon), with significant ecological ramifications. The increasing appreciation for the role of microbes in redox transformations of Fe is reflected in a recent surge in biological and environmental studies of microorganisms that conserve energy for growth from redox cycling of Fe compounds, particularly in the deep ocean. Here we highlight some of the key habitats where microbial Fe-oxidation plays significant ecological and biogeochemical roles in the oceanic regime, and provide a synthesis of recent studies concerning this important physiological group. We also provide the first evidence that microbial Fe-oxidizing bacteria are a critical factor in the kinetics of mineral dissolution at the seafloor, by accelerating dissolution by 6–8 times over abiotic rates. We assert that these recent studies, which indicate that microbial Fe-oxidation is widespread in the deep-sea, combined with the apparent role that this group play in promoting rock and mineral weathering, indicate that a great deal more attention to these microorganisms is warranted in order to elucidate the full physiological and phylogenetic diversity and activity of the neutrophilic Fe-oxidizing bacteria in the oceans.