Bacterial flora analysis of a microbial mat clogging the pipes of a well

Environmental heterogeneity may strongly influence the amount of heritable variation in phenotypic traits and thus affect evolutionary responses to natural selection. However, the question of whether heritabilities change across environmental gradients has received little empirical attention, particularly for wild vertebrates. We tested whether levels of heritable variation in body size, morphology and survival of juvenile Atlantic salmon (Salmo salar) differed between water flow regimes. We exposed individuals of known genetic relationships to rearing habitats characterized by slow and rapid water flows in a field experiment. We found that the additive genetic variation in body size tended to be higher for individuals reared under rapid water flows. By contrast, the heritabilities of other morphological traits were not consistently higher in either water flow. We also found that salmon grew faster under rapid water flows but also suffered high mortality rates with little heritable variation explaining the variation in survival. However, part of the variation in survival in the rapid water flow was explained by maternal effects. Our results suggest a strong tendency for heritable variation, particularly in body size to be revealed only under specific environmental conditions, such as those that allow for rapid growth. We provide support for the hypothesis that genotype by environment interactions have important effects on the adaptive potential of phenotypes in nature.

Bacteria thrive in nearly all environments on Earth, demonstrating remarkable adaptability to physical stimuli, as well as chemicals and light. However, the mechanisms by which bacteria locate and settle in ecological niches optimal for their growth remains poorly understood. Here, we show that Thermus thermophilus, a highly thermophilic non-flagellated species of bacteria, exhibits positive rheotaxis, navigating upstream in unidirectional rapid water flow. Mimicking their natural habitat at 70°C with a water current under optical microscopy, cells traveled distances up to 1 mm in 30 min, with infrequent directional changes. This long-distance surface migration is driven by type IV pili, facilitating vertical attachment at the cell pole, and shear-induced tilting of the cell body, resulting in alignment of the leading pole toward the direction of water flow. Direct visualization of type IV pili filaments and their dynamics revealed that rheotaxis is triggered by weakened attachment at the cell pole, regulated by ATPase activity, which was further validated by mathematical modeling. Flow experiments on 15 bacterial strains and species in the Deinococcota (synonym Deinococcus Thermus) phylum revealed that positive rheotaxis is highly conserved among rod-shaped Thermaceae, but absent in spherical-shaped Deinococcus. Our findings suggest that thermophilic bacteria reach their ecological niches by responding to the physical stimulus of rapid water flow, a ubiquitous feature in hot spring environments. This study highlights unforeseen survival strategies, showcasing an evolutionary adaptation to a surface-associated lifestyle where swimming bacteria would otherwise be swept away.

BackgroundFor decades it has been recognized that neutrophilic Fe-oxidizing bacteria (FeOB) are associated with hydrothermal venting of Fe(II)-rich fluids associated with seamounts in the world's oceans. The evidence was based almost entirely on the mineralogical remains of the microbes, which themselves had neither been brought into culture or been assigned to a specific phylogenetic clade. We have used both cultivation and cultivation-independent techniques to study Fe-rich microbial mats associated with hydrothermal venting at Loihi Seamount, a submarine volcano.Methodology/Principle FindingsUsing gradient enrichment techniques, two iron-oxidizing bacteria, strains PV-1 and JV-1, were isolated. Chemolithotrophic growth was observed under microaerobic conditions; Fe(II) and Fe0 were the only energy sources that supported growth. Both strains produced filamentous stalk-like structures composed of multiple nanometer sized fibrils of Fe-oxyhydroxide. These were consistent with mineralogical structures found in the iron mats. Phylogenetic analysis of the small subunit (SSU) rRNA gene demonstrated that strains PV-1 and JV-1 were identical and formed a monophyletic group deeply rooted within the Proteobacteria. The most similar sequence (85.3% similarity) from a cultivated isolate came from Methylophaga marina. Phylogenetic analysis of the RecA and GyrB protein sequences confirmed that these strains are distantly related to other members of the Proteobacteria. A cultivation-independent analysis of the SSU rRNA gene by terminal-restriction fragment (T-RF) profiling showed that this phylotype was most common in a variety of microbial mats collected at different times and locations at Loihi.ConclusionsOn the basis of phylogenetic and physiological data, it is proposed that isolate PV-1T ( = ATCC BAA-1019: JCM 14766) represents the type strain of a novel species in a new genus, Mariprofundus ferrooxydans gen. nov., sp. nov. Furthermore, the strain is the first cultured representative of a new candidatus class of the Proteobacteria that is widely distributed in deep-sea environments, Candidatus ζ (zeta)-Proteobacteria cl. nov.

This research investigated to reduce mass of heavy metals in AMD(acid mine drainage) by microbial mats formed on the channel bed. As, Cd, Cu, Fe, Mn and Zn components were monitored in water and microbial mats, at three points (AMD1, AMD2 and AMD3), in a total of six times. Average daily discharge mass of heavy metals was highest in July, Fe component contained more than 76% of total discharge mass. Discharge mass of heavy metals of AMD and heavy metal contents in microbial mats decreased with downstream at channel. Heavy metal components that average daily discharge mass is over 0.5 kg were Fe, Cu and Zn, and they were highest in July. Average removal efficiency of heavy metals in AMD was highest about 21% in Fe, this microbial mats were due to form from precipitation of Fe component in AMD by aerobic iron bacteria. Relative content for As component in microbial mats than AMD was over 16 times, this As components were due to absorb at iron oxide and iron hydroxide on the surface of microbial mats.

Microbial mats are occasionally reported in thermal springs and information on such mats is very scarce. In this study, microbial mats were collected from two hot springs (Brandvlei (BV) and Calitzdorp (CA)), South Africa and subjected to scanning electron microscopy (SEM) and targeted 16S rRNA gene amplicon analysis using Next Generation Sequencing (NGS). Spring water temperature was 55°C for Brandvlei and 58°C for Calitzdorp while the pH of both springs was slightly acidic, with an almost identical pH range (6.2–6.3). NGS analysis resulted in a total of 4943 reads, 517 and 736 OTUs for BV and CA at, respectively, a combined total of 14 different phyla in both samples, 88 genera in CA compared to 45 in BV and 37.64% unclassified sequences in CA compared to 27.32% recorded in BV. Dominant bacterial genera in CA microbial mat were Proteobacteria (29.19%), Bacteroidetes (9.41%), Firmicutes (9.01%), Cyanobacteria (6.89%), Actinobacteria (2.65%), Deinococcus‐Thermus (2.57%), and Planctomycetes (1.94%) while the BV microbial mat was dominated by Bacteroidetes (47.3%), Deinococcus‐Thermus (12.35%), Proteobacteria (7.98%), and Planctomycetes (2.97%). Scanning electron microscopy results showed the presence of microbial filaments possibly resembling cyanobacteria, coccids, rod‐shaped bacteria and diatoms in both microbial mats. Dominant genera that were detected in this study have been linked to different biotechnological applications including hydrocarbon degradation, glycerol fermentation, anoxic‐fermentation, dehalogenation, and biomining processes. Overall, the results of this study exhibited thermophilic bacterial community structures with high diversity in microbial mats, which have a potential for biotechnological exploitation.

Recent studies revealing exceptionally rapid water flow across graphene oxide membranes have highlighted them for potential filtration and separation applications. The physical and chemical features in graphene oxide membranes are heterogeneous, and there remains a great deal of speculation as to what is responsible for the facile water percolation. One potential contributing feature is the variation of interlayer spacing, which can occur naturally or be artificially induced. Herein, water flow across pristine, oxidized, and mixed membranes with interlayer distances of 0.7, 0.9, and 1.2 nm, corresponding respectively to the formation of discrete mono-, bi-, and trilayer water structures, was studied via molecular dynamics simulations. The interlayer spacing of 0.7 nm results in the formation of square ice for the pristine graphene membrane, which leads to collective motion, inhibiting equilibrium transport but allowing for rapid nonequilibrium flow comparable to that in the membranes with larger interlayer distances. A four-point time correlation function analysis of water structural relaxation reveals that collective water motions are responsible for rapid nonequilibrium flow for the interlayer spacing of 0.7 nm. Meanwhile, the central water layers formed in an interlayer spacing of 1.2 nm lead to almost entirely decoupled structure and dynamics between outer water layers.

Svalbard, situated in the high Arctic, is an important past and present coal mining area. Dozens of abandoned waste rock piles can be found in the proximity of Longyearbyen. This environment offers a unique opportunity for studying the biological control over the weathering of sulphide rocks at low temperatures. Although the extension and impact of acid mine drainage (AMD) in this area is known, the native microbial communities involved in this process are still scarcely studied and uncharacterized. Several abandoned mining areas were explored in the search for active AMD and a culture-independent approach was applied with samples from two different runoffs for the identification and quantification of the native microbial communities. The results obtained revealed two distinct microbial communities. One of the runoffs was more extreme with regards to pH and higher concentration of soluble iron and heavy metals. These conditions favored the development of algal-dominated microbial mats. Typical AMD microorganisms related to known iron-oxidizing bacteria (Acidithiobacillus ferrivorans, Acidobacteria and Actinobacteria) dominated the bacterial community although some unexpected populations related to Chloroflexi were also significant. No microbial mats were found in the second area. The geochemistry here showed less extreme drainage, most likely in direct contact with the ore under the waste pile. Large deposits of secondary minerals were found and the presence of iron stalks was revealed by microscopy analysis. Although typical AMD microorganisms were also detected here, the microbial community was dominated by other populations, some of them new to this type of system (Saccharibacteria, Gallionellaceae). These were absent or lowered in numbers the farther from the spring source and they could represent native populations involved in the oxidation of sulphide rocks within the waste rock pile. This environment appears thus as a highly interesting field of potential novelty in terms of both phylogenetic/taxonomic and functional diversity.

An analogue of matrix diffusion enhanced by biogenic redox reaction in fractured sedimentary rock

Microbial iron oxyhydroxides are common deposits in natural waters, recent sediments, and mine drainage systems. Along with these minerals, trace and rare earth elements (TREE) are being accumulated within the mineralizing microbial mats. TREE patterns are widely used to characterize minerals and rocks, and to elucidate their evolution and origin. However, whether and which characteristic TREE signatures distinguish between a biological and an abiological origin of iron minerals is still not well-understood. Here we report on long-term flow reactor studies performed in the Tunnel of Äspö (Äspö Hard Rock Laboratory, Sweden). The development of microbial mats dominated by iron-oxidizing bacteria (FeOB), namely Mariprofundus sp. and Gallionella sp were investigated. The feeder fluids of the flow reactors were tapped at 183 and 290 m below sea-level from two brackish, but chemically different aquifers within the surrounding, ~1.8 Ga old, granodioritic rocks. The experiments investigated the accumulation and fractionation of TREE under controlled conditions of the subsurface continental biosphere, and enabled us to assess potential biosignatures evolving within the microbial iron oxyhydroxides. After 2 and 9 months, concentrations of Be, Y, Zn, Zr, Hf, W, Th, Pb, and U in the microbial mats were 103- to 105-fold higher than in the feeder fluids whereas the rare earth elements and Y (REE+Y) contents were 104- and 106-fold enriched. Except for a hydrothermally induced Eu anomaly, the normalized REE+Y patterns of the microbial iron oxyhydroxides were very similar to published REE+Y distributions of Archaean Banded Iron Formations (BIFs). The microbial iron oxyhydroxides from the flow reactors were compared to iron oxyhydroxides that were artificially precipitated from the same feeder fluid. Remarkably, these abiotic and inorganic iron oxyhydroxides show the same REE+Y distribution patterns. Our results indicate that the REE+Y mirror closely the water chemistry, but they do not allow to distinguish microbially mediated from inorganic iron precipitates. Likewise, all TREE studied showed an overall similar fractionation behavior in biogenic, abiotic, and inorganic iron oxyhydroxides. Exceptions are Ni and Tl, which were only accumulated in the microbial iron oxyhydroxides and may point to a potential utility of these elements as microbial biosignatures.

Chemolithoautotrophic iron-oxidizing bacteria play an essential role in the global iron cycle. Thus far, the majority of marine iron-oxidizing bacteria have been identified as Zetaproteobacteria, a novel class within the phylum Proteobacteria. Marine iron-oxidizing microbial communities have been found associated with volcanically active seamounts, crustal spreading centers, and coastal waters. However, little is known about the presence and diversity of iron-oxidizing communities at hydrothermal systems along the slow crustal spreading center of the Mid-Atlantic Ridge. From October to November 2012, samples were collected from rust-colored mats at three well-known hydrothermal vent systems on the Mid-Atlantic Ridge (Rainbow, Trans-Atlantic Geotraverse, and Snake Pit) using the ROV Jason II. The goal of these efforts was to determine if iron-oxidizing Zetaproteobacteria were present at sites proximal to black smoker vent fields. Small, diffuse flow venting areas with high iron(II) concentrations and rust-colored microbial mats were observed at all three sites proximal to black smoker chimneys. A novel, syringe-based precision sampler was used to collect discrete microbial iron mat samples at the three sites. The presence of Zetaproteobacteria was confirmed using a combination of 16S rRNA pyrosequencing and single-cell sorting, while light micros-copy revealed a variety of iron-oxyhydroxide structures, indicating that active iron-oxidizing communities exist along the Mid-Atlantic Ridge. Sequencing analysis suggests that these iron mats contain cosmopolitan representatives of Zetaproteobacteria, but also exhibit diversity that may be uncommon at other iron-rich marine sites studied to date. A meta-analysis of publically available data encompassing a variety of aquatic habitats indicates that Zetaproteobacteria are rare if an iron source is not readily available. This work adds to the growing understanding of Zetaproteobacteria ecology and suggests that this organism is likely locally restricted to iron-rich marine environments but may exhibit wide-scale geographic distribution, further underscoring the importance of Zetaproteobacteria in global iron cycling.

We constructed a small flow chamber in which suboxic medium containing 60 to 120 muM FeCl(2) flowed up through a sample well into an aerated reservoir, thereby creating an suboxic-oxic interface similar to the physicochemical conditions that exist in natural iron seeps. When microbial mat material from the Marselisborg iron seep that contained up to 10 bacterial cells per cm (D. Emerson and N. P. Revsbech, Appl. Environ. Microbiol. 60:4022-4031, 1994) was placed in the sample well of the chamber, essentially all of the Fe flowing through the sample well was oxidized at rates of up to 1,200 nmol of Fe oxidized per h per cm of mat material. The oxidation rates of samples of the mat that were pasteurized prior to inoculation were only about 20 to 50% of the oxidation rates of unpasteurized samples. Sodium azide also significantly inhibited oxidation. These results suggest that at least 50% and up to 80% of the Fe oxidation in the chamber were actively mediated by the microbes in the mat. It also appeared that Fe stimulated the growth of the community since chambers fed with FeCl(2) accumulated masses of either filamentous or particulate growth, both in the sample well and attached to the walls of the chamber. Control chambers that did not receive FeCl(2) showed no sign of such growth. Furthermore, after 4 to 5 days the chambers fed with FeCl(2) contained 35 to 75% more protein than chambers not supplemented with FeCl(2). Leptothrix ochracea and, to a lesser extent, Gallionella spp. were responsible for the filamentous growth, and the sheaths and stalks, respectively, of these two organisms harbored large numbers of Fe-encrusted, nonappendaged unicellular bacteria. In chambers where particulate growth predominated, the unicellular bacteria alone appeared to be the primary agents of iron oxidation. These results provide the first clear evidence that the "iron bacteria" commonly found associated with neutral-pH iron seeps are responsible for most of the iron oxidation and that the presence of ferrous iron appears to stimulate the growth of these organisms.

Japanese Islands are covered with weathered volcanic rocks and soils. Terraced rice field are located in green-tuff areas which are very fertile but where landslides occur associated to strong earthquakes. The Xray diffraction and X-ray fluorescence analyses of the soils in landslide area identified predominant smectite and Mg, Al, Si, K, Ti, Mn and Fe are main components. The rice leaf showed that S, Cl, K and Ca play important roles for nutrients in the area. Drainpipe systems have set up in the green- tuff areas to reduce the risks of landslides. Reddish brown microbial mats inhabited bacteria and diatom in the drainpipe outlets. The microbial mats are rich in Fe and PO4(3-). The iron bacteria in the ground water have a high metabolic rate suggesting that the weathering materials were produced by not only physical and chemical influence but also by microorganism. Many microorganisms attach to mineral surfaces and show their high impact in the water mineral chemistry in the landslide area. Bacteria in the green-tuff over landslide area play important roles for sustainable agriculture including rice nutrition.

The rapid flow of water through soil macropores significantly affects the partitioning of precipitation between surface runoff and infiltration and also the rate of solute transport in soil, both of which have an impact on the risk of contamination of surface water and groundwater. The kinematic wave equation is often employed as a model of gravity-driven water flow through soil macropores. The exponent in this simple model influences the pore water velocity attained in the macropores at any given input rate and is usually estimated by inverse modelling against measured flow rates or water contents. In theory, the exponent in the kinematic wave equation should depend on the geometry and topology of the conducting macropore networks, although these relationships have not so far been investigated. In this study, we related metrics of soil structure derived from X-ray images to values of the kinematic exponent estimated from drainage experiments on twenty-two columns sampled at three different field sites under two contrasting land uses and at three different depths.We found that smaller values of the exponent in the kinematic wave equation, which would equate to more rapid flow of water through soil macropores, were found in plough pan and subsoil columns of smaller macroporosity, for which biopores comprised a significant fraction. The macroporosity in these columns was more vertically oriented and poorly inter-connected, though still continuous across the sample. In contrast, topsoil columns from both arable land and grassland had better connected, denser and more isotropically-distributed macropore networks and larger values of the kinematic exponent. Our results suggest that for predictive modelling at large scales, it may be feasible to estimate the kinematic exponent using class pedotransfer functions based on pedological information such as land use and horizon type.

Underwater plants are plants in the form of herbaceous plants and shrubs and low plants that cover the bottom of a forest area. Thus the function of the plant here is to withstand the destructive power of the falling rain fall and the rapid flow of water above the soil surface. Sibolangit Nature Park is a forest area with an area of ± 24.85 Ha. The existence of the lower plants in Sibolangit Nature Park become the main attraction for the visitors. The purpose of the research is to obtain the inventory data of the lower plants and describe the characters morphology. The research was conducted by using the exploration method along the path of Sibolangit Nature Park. From the research that has been done, there are 48 types of plants that consist of 31 families. Of the 48 undersea species identified, 30 of them belong to the Spermatophyta division, while the remaining 18 are included in the Pterydophyta division.Underwater plants are plants in the form of herbaceous plants and shrubs and low plants that cover the bottom of a forest area. Thus the function of the plant here is to withstand the destructive power of the falling rain fall and the rapid flow of water above the soil surface. Sibolangit Nature Park is a forest area with an area of ± 24.85 Ha. The existence of the lower plants in Sibolangit Nature Park become the main attraction for the visitors. The purpose of the research is to obtain the inventory data of the lower plants and describe the characters morphology. The research was conducted by using the exploration method along the path of Sibolangit Nature Park. From the research that has been done, there are 48 types of plants that consist of 31 families. Of the 48 undersea species identified, 30 of them belong to the Spermatophyta division, while the remaining 18 are included in the Pterydophyta division.

Abundant stromatolites have been found from the Neoproterozoic Jiudingshan and Niyuan formations in northern Jiangsu Province and northern Anhui Province, South China. The stromatolites are mostly stratiform, rarely small domed and conical (Conophyton-like), with more or less clearly laminated structures. Well-preserved, silicified microbial mats containing mat-building microfossils have been found in small domed, conical, and stratiform stromatolites of the Neoproterozoic Jiudingshan Formation and Niyuan Formation. Main mat-producing species are Gloeodiniopsis suxianensis among the coccoids, and Siphonophycus inornatum and Siphonophycus sp. among the filamentous cyanophytes, although Myxococcoides sp., Leiosphaeridia sp., and Eoentophysalis ­robusta are often included in the community. Present study indicates that the morphology of a microbial mat, particularly first microbial mat, plays an important role in the morphogenesis of stromatolites, and the community dominated by Gloeodiniopsis suxianensis, which is largely confined to stratiform stromatolites, may represent an intertide setting.