Mn(II)-oxidizing Bacteria are Abundant and Environmentally Relevant Members of Ferromanganese Deposits in Caves of the Upper Tennessee River Basin

The upper Tennessee River Basin contains the highest density of our nation's caves; yet, little is known regarding speleogenesis or Fe and Mn biomineralization in these predominantly epigenic systems. Mn:Fe ratios of Mn and Fe oxide-rich biofilms, coatings, and mineral crusts that were abundant in several different caves ranged from ca. 0.1 to 1.0 as measured using ICP-OES. At sites where the Mn:Fe ratio approached 1.0 this represented an order of magnitude increase above the bulk bedrock ratio, suggesting that biomineralization processes play an important role in the formation of these cave ferromanganese deposits. Estimates of total bacterial SSU rRNA genes in ferromanganese biofilms, coatings, and crusts measured approximately 7×10⁷–9×10⁹ cells/g wet weight sample. A SSU-rRNA based molecular survey of biofilm material revealed that 21% of the 34 recovered dominant (non-singleton) OTUs were closely related to known metal-oxidizing bacteria or clones isolated from oxidized metal deposits. Several different isolates that promote the oxidation of Mn(II) compounds were obtained in this study, some from high dilutions (10^–8–10^–10) of deposit material. In contrast to studies of caves in other regions, SSU rRNA sequences of Mn-oxidizing bacterial isolates in this study most closely matched those of Pseudomonas, Leptothrix, Flavobacterium, and Janthinobacterium. Combined data from geochemical analyses, molecular surveys, and culture-based experiments suggest that a unique consortia of Mn(II)-oxidizing bacteria are abundant and promoting biomineralization processes within the caves of the upper Tennessee River Basin.     

辽宁朝阳马山洞的食肉类化石

本文主要记述了辽宁省朝阳市龙城区马山洞发现的食肉类化石。堆积物的上部主要为颗粒细小的砂质黏土, 而下部主要为直径较大的角砾。2007年出土的食肉目化石有: 似浣熊貉(Nyctereutes procyonoides)、赤狐(Vulpes vulpes)、狗獾(Meles meles)、黄鼬(Mustela sibirica)、中华猫(Felis chinensis)和疑似虎(Panthera tigris)?。其中前5个种在形态上与现生种类非常接近; 而最后一个种除与现生虎比较接近外, 与现生狮子也有一定的相似性。     

Geomicrobiology and Redox Geochemistry of the Karstified Miocene Gypsum Aquifer,Western Ukraine: The Study from Zoloushka Cave

The gypsum karst of the western Ukraine developed largely under artesian conditions. The Miocene aquifer is presently entrenched and dewatered over much of the territory, while it remains confined in the zone adjacent to the Carpathian Foredeep. The most prominent geochemical features of the Miocene aquifer system in the confined karst zone are: (1) the almost universal presence of a bioepigenetic calcite bed, enriched in the light carbon isotope, at the top of the gypsum (the "Ratynsky Limestone"), (2) the widespread sulfur mineralization associated with the above calcite bed (the region is one of the world's largest sulfur-bearing basins), and (3) high H 2 S and CO 2 in the groundwater. Intense microbial sulfate-reduction processes occur in the gypsum in this zone. Zoloushka Cave is the third longest (92 km) and the largest by volume (more than 7 2 10 5 m 3 ) gypsum cave in the world. It is a unique example of a young artesian cave that only during the Holocene became partly drained and during the last 50 years progressively dewatered due to a quarry operation. These rapid changes have induced a number of transitional geochemical processes, some of which appear to be bacterially mediated. Six groups of microorganisms have been identified in the cave. Our article discusses the aquifer geochemistry during the transitional stage in the light of the microbiological studies.     

河南织机洞旧石器遗址的洞穴堆积和沉积环境分析

MIS3阶段晚期是末次冰期中一个气候比较温暖的间冰阶,当时人类活动相当活跃,在世界各地这一时期的人类文化遗址不仅数量多,而且文化面貌也发生明显的变化。织机洞遗址是一处以旧石器时代中晚期为主的洞穴遗址,洞穴中堆积地层可以划分为四层:下部含丰富的打制石器称下文化层,属旧石器中晚期;中部不含石器;上部含少量打制石器称中文化层,属旧石器晚期;顶部含有裴李岗和秦汉时期的文化遗存称上文化层,属全新世时期。根据光释光年代测定,文化遗存最为丰富的下文化层,年龄为距今3·5—5万年,相当于MIS3阶段的中晚期,正处于"旧石器晚期革命"的前夕。孢粉分析结果表明,下文化层所处的MIS3阶段气候比较温暖湿润,为暖温带草原-疏树草原环境,良好的气候环境有利于当时古代人类的生存与繁衍。     

Stratigraphy, U-Th chronology, and paleoenvironments at Gladysvale Cave: insights into the climatic control of South African hominin-bearing cave deposits

Gladysvale Cave is one of the few Plio-Pleistocene hominin-bearing cave sites in South Africa that contains a well-stratified cave fill with clastic sediments interspersed with flowstones. The clastic sediments can be divided into units based on the presence of intercalated flowstones, forming flowstone bounded units (FBU). Ten MC-ICP-MS uranium-series dates on several flowstone horizons in the Gladysvale Internal Deposit fan indicate deposition from the late mid-Pleistocene ( approximately 570 ka) to Holocene ( approximately 7 ka) during limited periods of higher effective moisture. Clastic sedimentation occurred during the interceding, presumably more arid, periods. This sequence is not consistent with earlier models for South African caves that simply assumed interglacial sedimentation and glacial erosion. (13)C/(12)C data suggest that flowstone tended to form during periods with higher proportions of C(3) plants in the local vegetation, while clastic sediments reflect higher proportions of C(4) grasses, although this is not always the case. We argue that flowstones are precipitated during periods of higher effective precipitation and restricted cave entrances, while clastic sediments accumulated during periods with more open vegetation. The sedimentary fill of the fossiliferous deposits are, therefore, highly episodic in nature, with large periods of time unlikely to be represented. This has serious implications for the other hominin-bearing caves close by, as these deposits are likely to be similarly episodic. This is especially pertinent when addressing extinction events and reconstructions of paleoenvironments, as large periods of time may be unrecorded. The Gladysvale Cave fill sediments may serve as a climatically forced chronostratigraphic model for these less well-stratified and well-dated Plio-Pleistocene sites.     

Identification and characterization of microbial biofilm communities associated with corroded oil pipeline surfaces

Microbially influenced corrosion (MIC) has long been implicated in the deterioration of carbon steel in oil and gas pipeline systems. The authors sought to identify and characterize sessile biofilm communities within a high-temperature oil production pipeline, and to compare the profiles of the biofilm community with those of the previously analyzed planktonic communities. Eubacterial and archaeal 16S rRNA sequences of DNA recovered from extracted pipeline pieces, termed ‘cookies,’ revealed the presence of thermophilic sulfidogenic anaerobes, as well as mesophilic aerobes. Electron microscopy and elemental analysis of cookies confirmed the presence of sessile cells and chemical constituents consistent with corrosive biofilms. Mass spectrometry of cookie acid washes identified putative hydrocarbon metabolites, while surface profiling revealed pitting and general corrosion damage. The results suggest that in an established closed system, the biofilm taxa are representative of the planktonic eubacterial and archaeal community, and that sampling and monitoring of the planktonic bacterial population can offer insight into biocorrosion activity. Additionally, hydrocarbon biodegradation is likely to sustain these communities. The importance of appropriate sample handling and storage procedures to oilfield MIC diagnostics is highlighted.     

Bacterial and Fungal Diversity of Quaternary Cave Sediment Deposits

The bacterial and fungal assemblages of clastic sediments collected from two caves located in north-western Romania were investigated by assessing ITS and 16S rRNA gene diversity. Bacterial members belonging to Chloroflexi, Nitrospirae, Proteobacteria, Firmicutes, Acidobacteria, Gemmatimonadetes, and fungal members of Ascomycota were identified. Except for Bacillus sp., all bacteria were related to uncultured or unknown species and the majority (86%) of the bacterial sequences from one of the caves had no close GenBank relatives. The bacterial sequences obtained clustered with species found in extreme environments. Half of the bacterial operational taxonomic units were clustered with clones isolated from deep subsurface sediments of a radioactively contaminated site in the USA. The present study represents the first attempt to identify microorganisms in Quaternary cave sediments.

Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file.     

Electrochemical concepts and techniques in the study of stainless steel ennoblement

Electrochemical theory and technique used to investigate microbially influenced corrosion is discussed with a focus on methods used to demonstrate the manganic-oxide mechanism of stainless steel Ennoblement. The concept of mixed potential and its relationship to the current-voltage behavior of stainless steel is developed. This concept is used to interpret microbially induced changes in corrosion potential, polarization behavior, surface-oxide abundance, and the redox environment at submerged metal surfaces. Microelectrode, capacitance, and coulometric methods are described that can be used to discriminate electrochemical effects caused by changes in solution properties from those caused by mineral deposition at the metal surface. The variety of electrochemical, wet-chemical, microbiological, and surface analytical techniques used to demonstrate the effect of biomineralized manganese dioxide on the electrochemical behavior of stainless steel are summarized.     

岩溶洞穴苔藓群落特征及其对重金属污染的指示意义: 以贵州织金洞为例

岩溶洞穴的开发与利用导致的重金属污染严重威胁洞穴环境及地下水, 因此对洞穴环境的监测具有重要的现实意义。本文通过对典型的暗河型溶洞贵州织金洞内的苔藓群落特征及其重金属污染状况进行研究, 拟揭示苔藓群落对洞穴重金属污染的指示意义。共发现苔藓群落类型34个, 苔藓植物种类20科33属49种, 含苔类8科8属12种, 藓类12科25属37种。优势科为丛藓科、凤尾藓科和提灯藓科, 物种占比率分别为16%、14%、14%。Hg污染超标倍数最高达59.45倍, 在距洞口不同深度均远高于Cr和Zn, 说明洞内Hg污染较为严重。苔藓群落指标随着重金属污染含量的上升总体呈下降趋势。所测定的重金属中基质Hg含量与苔藓群落指标的拟合程度最好, 与其对应的苔藓群落指标均呈显著负相关关系(P < 0.05), 说明苔藓群落特征能够很好地反映洞内Hg污染的变化趋势。RDA排序结果分析表明: 洞穴苔藓群落为适应低光度环境会表现出向光性运动、喜钙生基质、耐重金属等生理特征。蛇苔(Conocephalum conicum)植物体内的Hg含量与其基质Hg含量具有显著相关性(P < 0.05), 说明蛇苔受基质Hg污染影响较大。在今后的治理过程中, 可以考虑将蛇苔作为洞内环境的生物监测材料之一。     

Habitat and Population Data of Troglobitic Armored Cave Catfish, Ancistrus Cryptophthalmus Reis, 1987, from Central Brazil (Siluriformes: Loricariidae)

Population ecology of the troglobitic armored catfish, A. cryptophthalmus, from caves in São Domingos karst area of central Brazil, was studied in a two-census capture-mark-recapture study carried out during the dry season of 1999. Like many loricariids, including epigean Ancistrus catfishes from that area, A. cryptophthalmus is a typical bottom-dweller with a strong preference for rocky substrates in fast-flowing stream sectors. Relatively high population densities, when compared to other cavefishes, were recorded in the studied cave sections: 0.9 individuals m^–2 in Angélica Cave and 0.5 individuals m^–2 in Passa Três Cave. Passa Três Stream is a small tributary of the São Vicente Cave system, and the estimated population for Passa Três Cave (ca. 2000 m long) is around 1000 individuals. On the other hand, the large Angélica Cave Stream (8 km long) harbors a very large population, conservatively estimated at 20 000 individuals. No fish movements of distances longer than 100 m were recorded in the 40-day period. In Passa Três Cave, a few movements of distances up to 60 m were detected. Proportion of mature females in Angélica Cave was higher than in Passa Três Cave, possibly reflecting a greater food availability in the first cave. Mean individual growth rates in Angélica Cave (1.35 mm month^–1 for size class <41 mm SL, 0.17 mm month^–1 for size class >41 mm SL) point to relatively high longevities, possibly attaining 15 years.     

Relationship Between Periodic Resuspension Events and Planktonic Diatom Community Structure in Lake Michigan: A Field and Laboratory Investigation

Lake Michigan provides an ideal location for comparing episodic physical forcing events (storms) on phytoplankton processes and the more persistent seasonal variability of phytoplankton communities. This is due to the duration and extent of the highly turbid, recurrent coastal plume (RCP) in the lake during the winter/early spring. Although the RCP can coincide with the initiation of the basin wide spring diatom bloom, linkages between the duration and intensity of the plume and the prominent role of light availability in regulating Lake Michigan phytoplankton growth during the spring isothermal period have been postulated, but not verified. The concurrent physical and biological events provide a novel opportunity to examine phenomena associated with the RCP affecting the distribution and abundance of species in Lake Michigan's planktonic diatom flora. In this study, planktonic diatom assemblages from pre, post and active spring plume events were examined from stations along Lake Michigan's southern shoreline. Species abundance changed rapidly during storm events. Sediment resuspension via storm activity created a suboptimal growth environment. Post‐storm event diatom phytoplankton communities were floristically distinct from prestorm event communities, with resting cell‐forming taxa playing a significant role in these community‐restructuring periods. Laboratory simulations of resuspension events using Lake Michigan sediments were conducted under a variety of environmental conditions. Parameters varied included day length, temperature, and silica. The resulting assemblages were quantitatively counted. A statistically significant relationship was identified between day length and the vegetative growth of many resting cell‐forming diatom species. When day length was calculated for poststorm event field data, it revealed a high correlation between poststorm event communities and those predicted by the laboratory simulations. Timing of storm events and latitudinal position of the aquatic system are then important elements for consideration when predicting diatom phytoplankton community structure due to the relationship these factors have with day length.     

Initial excavation and dating of Ngalue Cave: A Middle Stone Age site along the Niassa Rift, Mozambique

Direct evidence for a systematic occupation of the African tropics during the early late Pleistocene is lacking. Here, we report a record of human occupation between 105-42 ka, based on results from a radiometrically-dated cave section from the Mozambican segment of the Niassa (Malawi/Nyasa) Rift called Ngalue. The sedimentary sequence from bottom to top has five units. We concentrate on the so-called “Middle Beds,” which contain a Middle Stone Age industry characterized by the use of the discoidal reduction technique. A significant typological feature is the presence of formal types such as points, scrapers, awls, and microliths. Special objects consist of grinders/core-axes covered by ochre. Ngalue is one of the few directly-dated Pleistocene sites located along the biogeographical corridor for modern human dispersals that links east, central, and southern Africa, and, with further study, may shed new light on hominin cave habitats during the late Pleistocene.     

A novel qPCR protocol for the specific detection and quantification of the fuel-deteriorating fungus Hormoconis resinae

A wide variety of fungi and bacteria are known to contaminate fuels and fuel systems. These microbial contaminants have been linked to fuel system fouling and corrosion. The fungus Hormoconis resinae, a common jet fuel contaminant, is used in this study as a model for developing innovative risk assessment methods. A novel qPCR protocol to detect and quantify H. resinae in, and together with, total fungal contamination of fuel systems is reported. Two primer sets, targeting the markers RPB2 and ITS, were selected for their remarkable specificity and sensitivity. These primers were successfully applied on fungal cultures and diesel samples demonstrating the validity and reliability of the established qPCR protocol. This novel tool allows clarification of the current role of H. resinae in fuel contamination cases, as well as providing a technique to detect fungal outbreaks in fuel systems. This tool can be expanded to other well-known fuel-deteriorating microorganisms.     

A new and morphologically distinct population of cavernicolous Poecilia mexicana (Poeciliidae: Teleostei)

The cave molly, Poecilia mexicana, from the Cueva del Azufre, a sulfur cave in Tabasco, Mexico, ranks among the best-studied cave fishes worldwide, despite being known from a single population only. Here we describe a newly discovered second population of cave-dwelling P. mexicana from a nearby, but mostly non-sulfidic cave (Luna Azufre). Despite apparent similarities between the two populations (such as reduced eye diameter and reduced pigmentation), a geometric morphometric analysis revealed pronounced morphological differentiation between the two cave forms.     

湖北建始高坪洞穴调查及其试掘简报

高坪位于湖北省建始县东北部, 长江支流清江流域上游。该区域地处扬子地台中段北缘,区内中生界灰岩发育,新生代以来的构造运动和气候条件有利于岩溶的发育和洞穴形成,山盆期夷平面保存完好。2008年4—5月间, 考察队对该区域进行了为期近一个月的洞穴调查和试掘。对16处洞穴的调查表明,该区域在700m—950m高度发育有较多的更新世洞穴堆积物, 其中洞槽、神牛洞、响水寨洞和左家硝洞等洞穴工作条件较好, 是下一步发掘工作的重点。对巨猿洞东洞口外和大岩洞的试掘表明, 这里蕴藏着较多的动物化石和早期人类活动的遗物, 可进一步发掘和研究。     

Cytochrome P450 1A induction in gudgeon Gobio gobio : Laboratory and Field Studies

The induction of cytochrome P450 1A was studied in gudgeon (Gobio gobio), a common European cyprinid, using both farm-raised and field-caught fish. The effects of sex, reproductive status and past exposure to xenobiotics were assessed. When exposed to beta-naphthoflavone (bNF), reared gudgeon showed a dose-dependent increase of EROD activity with a plateau observed at doses from 20 mg kg-1 (females) and 5 mg kg-1 (males). The sexual difference in EROD activity was related to the gonadosomatic index (GSI) of the female whatever the level of induction. Dose and sex effects were confirmed by the immunodetection of CYP1A protein. More than 1 month was necessary for EROD activity to decrease to baseline levels. A second bNF injection after 32 days gave similar levels of induction, suggesting that EROD induction by bNF was not impaired by a pretreatment. Wild fish were brought from two sites in the Rhone river basin: a low contaminated site (Ain) and a highly contaminated site (Rhone). Wild gudgeon were highly induced by bNF in laboratory conditions, except males from the Rhone site which exhibited EROD levels as high as the EROD plateau found in laboratory conditions. A 2- month depuration period in clean water was necessary for EROD activity in wild gudgeon to decrease to baseline levels. These results provide better knowledge of the main factors of modulation of the induction in gudgeon as well as on the influence of the history of exposure to inducers.     

Field and Laboratory Studies on some Photosynthetic Bacteria in Aswan High Dam Lake. II. Isolation and Identification of Purple Non-sulfur Bacteria (Rhodospirillaceae)

485 isolates were recorded from different localities between summer 1984 and spring 1985. These isolates comprise five different genera with eight different species of purple non-sulfur bacteria- Rhodopseudomonas was the most common genus at all sites and was represented by three species. R. acidophila, R. blastica, R. palustris. Rhodomicrobium was the second in frequency and was represented by R. vannielli only. This species was only recorded for khor sites. Rhodocyclus was represented by two species, R. gelatinosus and R. tenuis. Rhodobacter and Rhodospirillum were represented by one species each, Rhodobacter capsulatus and Rhodospirillum rubrum. Khor sites were richer in number of isolates and genera of purple non-sulphur bacteria than the main body of AHDL. Some species were more common in winter and spring while others predominate in summer and autumn.     

A carbonate corrosion experiment at a marine methane seep: The role of aerobic methanotrophic bacteria

Methane seeps are typified by the formation of authigenic carbonates, many of which exhibit corrosion surfaces and secondary porosity believed to be caused by microbial carbonate dissolution. Aerobic methane oxidation and sulfur oxidation are two processes capable of inducing carbonate corrosion at methane seeps. Although the potential of aerobic methanotrophy to dissolve carbonate was confirmed in laboratory experiments, this process has not been studied in the environment to date. Here, we report on a carbonate corrosion experiment carried out in the REGAB Pockmark, Gabon-Congo-Angola passive margin, in which marble cubes were deployed for 2.5 years at two sites (CAB-B and CAB-C) with apparent active methane seepage and one site (CAB-D) without methane seepage. Marble cubes exposed to active seepage (experiment CAB-C) were found to be affected by a new type of microbioerosion. Based on 16S rRNA gene analysis, the biofilms adhering to the bioeroded marble mostly consisted of aerobic methanotrophic bacteria, predominantly belonging to the uncultured Hyd24-01 clade. The presence of abundant ¹³C-depleted lipid biomarkers including fatty acids (n-C_16:1ω8c, n-C_18:1ω8c, n-C_16:1ω5t), various 4-mono- and 4,4-dimethyl sterols, and diplopterol agrees with the dominance of aerobic methanotrophs in the CAB-C biofilms. Among the lipids of aerobic methanotrophs, the uncommon 4α-methylcholest-8(14)-en-3β,25-diol is interpreted to be a specific biomarker for the Hyd24-01 clade. The combination of textural, genetic, and organic geochemical evidence suggests that aerobic methanotrophs are the main drivers of carbonate dissolution observed in the CAB-C experiment at the REGAB pockmark.     

On the Potential Contribution of Microfungi to the Decomposition of Reed Leaf Detritus in a Coastal Lagoon: A Laboratory and Field Experiment

The potential contribution of microfungi to reed decomposition in a coastal habitat (Le Cesine Lagoon, Italy) was investigated under laboratory and field conditions. Leaf pack mass and surface loss, ergosterol content and O₂ uptake were used to construct carbon budgets and an empirical ergosterol‐to‐O₂ uptake relationship based on literature data was used to estimate the contribution of microfungi. Under laboratory conditions, reed carbon loss was entirely due to leaching and microbial respiration. In contrast, C losses observed in the field were accounted for by microbial respiration and macroinvertebrate shredding almost equally. Microfungi were estimated to account for 98% and 69% of microbially‐respired carbon under laboratory and field conditions, respectively. Our results provide a preliminary, quantitative assessment of microfungal contribution to reed decomposition in brackish habitats. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)