Organic-rich bimineralic ooids record biological processes in Shark Bay,Western Australia

Marine ooids have formed in microbially colonized environments for billions of years, but the microbial contributions to mineral formation in ooids continue to be debated. Here we provide evidence of these contributions in ooids from Carbla Beach, Shark Bay, Western Australia. Dark 100–240 μm diameter ooids from Carbla Beach contain two different carbonate minerals. These ooids have 50–100 μm-diameter dark nuclei that contain aragonite, amorphous iron sulfide, detrital aluminosilicate grains and organic matter, and 10–20 μm-thick layers of high-Mg calcite that separate nuclei from aragonitic outer cortices. Raman spectroscopy indicates organic enrichments in the nuclei and high-Mg calcite layers. Synchrotron-based microfocused X-ray fluorescence mapping reveals high-Mg calcite layers and the presence of iron sulfides and detrital grains in the peloidal nuclei. Iron sulfide grains within the nuclei indicate past sulfate reduction in the presence of iron. The preservation of organic signals in and around high-Mg calcite layers and the absence of iron sulfide suggest that organics stabilized high-Mg calcite under less sulfidic conditions. Aragonitic cortices that surround the nuclei and Mg-calcite layers do not preserve microporosity, iron sulfide minerals nor organic enrichments, indicating growth under more oxidizing conditions. These morphological, compositional, and mineralogical signals of microbial processes in dark ooids from Shark Bay, Western Australia, record the formation of ooid nuclei and the accretion of magnesium-rich cortical layers in benthic, reducing, microbially colonized areas.     

Cryogenic Minerals in Hawaiian Lava Tubes: A Geochemical and Microbiological Exploration

The Mauna Loa volcano, on the Island of Hawaii, has numerous young lava tubes. Among them, two at high altitudes are known to contain ice year-round: Mauna Loa Icecave (MLIC) and the Arsia Cave. These unusual caves harbor cold, humid, dark, and biologically restricted environments. Secondary minerals and ice were sampled from both caves to explore their geochemical and microbiological characteristics. The minerals sampled from the deep parts of the caves, where near freezing temperatures prevail, are all multi-phase and consist mainly of secondary amorphous silica SiO₂, cryptocrystalline calcite CaCO₃, and gypsum CaSO₄·2H₂O. Based on carbon and oxygen stable isotope ratios, all sampled calcite is cryogenic. The isotopic composition of falls on the global meteoric line, indicating that little evaporation has occurred. The microbial diversity of a silica and calcite deposit in the MLIC and from ice pond water in the Arsia Cave was explored by analysis of ～50,000 small subunit ribosomal RNA gene fragments via amplicon sequencing. Analyses reveal that the Hawaiian ice caves harbor unique microbial diversity distinct from other environments, including cave environments, in Hawaii and worldwide. Actinobacteria and Proteobacteria were the most abundant microbial phyla detected, which is largely consistent with studies of other oligotrophic cave environments. The cold, isolated, oligotrophic basaltic lava cave environment in Hawaii provides a unique opportunity to understand microbial biogeography not only on Earth but also on other planets.     

Hypolithic Cyanobacteria Supported Mainly by Fog in the Coastal Range of the Atacama Desert

The Atacama Desert is one of the driest places on Earth, with an arid core highly adverse to the development of hypolithic cyanobacteria. Previous work has shown that when rain levels fall below ~1 mm per year, colonization of suitable quartz stones falls to virtually zero. Here, we report that along the coast in these arid regions, complex associations of cyanobacteria, archaea, and heterotrophic bacteria inhabit the undersides of translucent quartz stones. Colonization rates in these areas, which receive virtually no rain but mainly fog, are significantly higher than those reported inland in the hyperarid zone at the same latitude. Here, hypolithic colonization rates can be up to 80%, with all quartz rocks over 20 g being colonized. This finding strongly suggests that hypolithic microbial communities thriving in the seaward face of the Coastal Range can survive with fog as the main regular source of moisture. A model is advanced where the development of the hypolithic communities under quartz stones relies on a positive feedback between fog availability and the higher thermal conductivity of the quartz rocks, which results in lower daytime temperatures at the quartz–soil interface microenvironment.     

Colonization,variability, and the use of substratum-filled trays for biomonitoring benthic communities

Sampling variability and colonization rate of introduced substrates (plastic trays filled with pebble and cobble) in two southwestern Virginia streams are described. Substrates were rapidly colonized by aquatic macroinvertebrates, but colonization rates differed between years, possibly due to annual variability in macroinvertebrate abundance. To examine the applicability of using these substrates for biomonitoring benthic communities, trays were placed at several locations in a river receiving power plant discharges. Only six samples were necessary to detect a 15%reduction in macroinvertebrate density and a 12% reduction in number of taxa at effluent sites. Benthic communities established on rock-filled trays and multiplate samplers collected from the same stations during the same period were compared. Although multiplate samplers were more variable than rock trays and were selective for different taxa, both substrate types showed significant differences in community parameters among locations. Rock trays at all sites were dominated by Cheumatopsyche sp., whereas chironomids were more abundant on multiplate samplers. The relative abundance of mayflies was reduced at the effluent site on both substrate types.     

Unravelling the microbial role in ooid formation – results of an in situ experiment in modern freshwater Lake Geneva in Switzerland

The microbial role in the formation of the cortex of low‐Mg calcite freshwater ooids in western part of Lake Geneva in Switzerland has been suggested previously, but not demonstrated conclusively. Early work mostly concentrated in hypersaline milieus, and hence little is known about their genesis in freshwater environments. We designed an in situ experiment to mimic the natural process of low‐Mg calcite precipitation. A special device was placed in the ooid‐rich bank of the lake. It contained frosted glass (SiO₂) slides, while quartz (SiO₂) is the most abundant mineral composition of ooid nuclei that acted as artificial substrates to favour microbial colonization. Microscopic inspection of the slides revealed a clear seasonal pattern of carbonate precipitates, which were always closely associated with biofilms that developed on the surface of the frosted slides containing extracellular polymeric substance, coccoid and filamentous cyanobacteria, diatoms and heterotrophic bacteria. Carbonate precipitation peaks during early spring and late summer, and low‐Mg calcite crystals mostly occur in close association with filamentous and coccoid cyanobacteria (e.g. Tolypothrix, Oscillatoria and Synechococcus, Anacystis, respectively). Further scanning electron microscope inspection of the samples revealed low‐Mg calcite with crystal forms varying from anhedral to euhedral rhombohedra, depending on the seasons. Liquid cultures corroborate the in situ observations and demonstrate that under the same physicochemical conditions the absence of biofilms prevents the precipitation of low‐Mg calcite crystals. These results illustrate that biofilms play a substantial role in low‐Mg calcite ooid cortex formation. It further demonstrates the involvement of microbes in the early stages of ooid development. Combined with ongoing microbial cultures under laboratory‐controlled conditions, the outcome of our investigation favoured the hypothesis of external microbial precipitation of low‐Mg calcite as the main mechanism involved in the early stage of ooid formation in freshwater Lake Geneva.     

Export of species to islands from sources of differing maturity

Export of species from sources (epicenters) of differing ages and complexities was examined using laboratory microcosms. Polyurethane foam (PF) artificial substrates were colonized by protozoans for different time periods in a small pond. Substrates were returned to the laboratory and used as epicenters for protozoan colonization of barren PF islands in initially sterile microcosms. Islands were exposed to epicenters for either 24 h or continuously for 28 d. Islands from pairs of microcosms exposed to epicenters of identical ages were sampled on 1, 3, 7, 14, 21, 28 and 46 d after initial epicenter exposure. Colonization parameters were estimated by fitting numbers of colonizing species to the MacArthur-Wilson equilibrium model. Islands exposed continuously to epicenters were colonized by significantly more species than those exposed for only 24 h. Islands exposed to immature, species poor epicenters were colonized by a greater proportion of the source community than those exposed to more mature, species rich epicenters. All islands were depauperate compared to epicenters except those exposed to the most immature (1 d old) epicenter. Colonization continued at a reduced rate in spite of the absence of the epicenter. Results from communities with rapid species turnover and rapidly reproducing species suggest that the continuous presence of a species source is less important for colonization of a new habitat. Dispersal of potential colonists occurs rapidly in these communities. Less mature communities dominated by pioneer forms are more effective at producing colonists than more mature communities.     

Colonization and degradation of rubber pieces by Nocardia sp.

The growth of a Nocardia sp. occurs essentially on the insoluble rubber substrate and the cells are tightly bound to the rubber in the initial stage of the growth in spite of vigorous stirring of the cultures. The colonization of rubber pieces was followed by staining with Schiff reagent, and it was revealed that not only the thickness of rubber pieces, but also their length and width greatly influenced microbial colonization and degradation of natural rubber products. Among rubber pieces of various shapes, long strips were most rapidly covered by many microbial colonies and experienced the highest rate of rubber degradation. The rate of degradation (expressed by % weight loss) of the long strips of rubber was a linear function of surface area per unit weight of rubber. Thin and wide films of rubber were also rapidly colonized and degraded, while the colonization and degradation of short and narrow pieces were substantially slower and less extensive.     

DIATOM COLONIZATION ON ARTIFICIAL SUBSTRATA IN POOL AND RIFFLE ZONES STUDIED BY LIGHT AND SCANNING ELECTRON MICROSCOPY1

Light and scanning electron microscopy were utilized to quality diatom colonization in Oak Creek, Arizona. Aluminum SEM stubs with and without plexiglass discs were anchored into rocks. Early colonization on five stub microzones was examined at hourly intervals; weekly intervals of up to 3 wk were employed to record community development in pool find riffle. Plexiglass was more suitable for microbial colonization than aluminum. Organic matter and bacteria were important surface pre-conditioning agents while fungi were instrumental in trap/ting cells during early stages of colonization in the riffle. Diatom colonization was initialed within 1 h on the upstream side of substrata in riffles, while the tap face was colonized first in pools. Colonization moved rapidly to the perimeter in each system. Early colonization of-side microzones was considerably more asymmetric in the riffle than, pool. At Idler stages (2 wk) diatoms with their associated mucilage and algal filaments contributed to the stability of the microbial communities. Horizontally positioned species (Achnanthes, Cocconeis) were early colonizers in both systems while vertically positioned species (Gomphonema, Nitzschia) were more important in later successional stages (3 wk) in the riffle. Horizontally positioned species remained dominant throughout the 3 wk period in the pool. After 3 wk, diversity was normally greater in the pool while density was higher in the riffle. Detrital microcosms containing viable microbiol assemblages frequently collected on tin-upstream face of substrata in the riffle. The random nature by which these detrital microcoms contact downstream substrata greatly contribute to the spatial variation of periphyton in streams. These detrital microcosms expedite repeated colonization in lotic systems.     

空间层次及人工基质对着生藻类建群特性的影响

为全面了解着生藻类在建群中群落变化的生态学特性,揭示着生藻类的建群规律,在以丝状藻类为优势藻的生态塘中,采用花岗岩和瓷砖为附着材料,设置水体底部和中部为附着位点,进行频次为10d的采样分析。结果表明,生态塘中共检出8门73属117种着生藻类,其中以硅藻、蓝藻、绿藻为优势类群。同时不同人工基质和不同空间层次条件下着生藻类的建群特征较一致,早期以单细胞硅藻如舟形藻(Navicula sp.)、脆杆藻(Fragilaria sp.)、曲壳藻(Achnanthes sp.)等为优势,后期以丝状藻类如鞘丝藻(Lyngbya sp.)、颤藻(Oscillatoria sp.)、伪鱼腥藻(Pseudanabaena sp.)等为优势;研究结果发现不同人工基质(花岗岩和瓷砖)对着生藻类的种类组成、细胞密度、生物量和藻类多样性无显著影响,花岗岩和瓷砖上附着的着生藻类具有较高的相似性;但不同的空间层次对着生藻类建群特征影响明显,水体底部具有更多的硅藻种类数,中部具有更多的绿藻,随着建群时间的发展,蓝藻比例不断增加;就生物量而言,底部的着生藻类叶绿素a显著高于水体中部,但两者的细胞密度无显著性差异;随着建群过程的发展,水体底部的着生藻类生物量达峰值所需的时间比中部更长。通过相关性分析,生态塘中着生藻类的生长主要受总磷的影响。     

Transmission Electron Microscopic Observation of Mercury-Bearing Bacterial Clay Minerals in a Small-Scale Gold Mine in Tanzania

Mercury is a toxic substance that is widely distributed throughout the hydrosphere, biosphere, and lithosphere. Mine waste environments and mine waters support a wide diversity of microbial life. The microbial ecology of environments where mine waters are polluted with heavy metals is poorly understood. Here, we describe the features of bacteria in mercury-contaminated gold panning ponds in a small-scale gold mine (Geita) near Lake Victoria, Tanzania using energy filtering transmission electron microscopy (EF-TEM) and scanning transmission electron microscopy equipped with energy dispersive X-ray spectroscopy (STEM-EDX). Most bacteria in the panning pond showed thick exopolysaccharides (EPSs), and many clay minerals attached onto the surface of EPSs. The clay minerals and EPSs might act as protective layers for the bacteria against toxic materials. The clay minerals were composed of smectite, halloysite, and kaolinite associated with calcite and goethite. Scanning electron microscopy equipped with energy dispersive X-ray spectroscopy indicated that the bulk soil samples contained abundant Si, Al, K, Ca, and Fe with heavy metals such as Au, Ti, and Ag. The results indicate that Hg pollution from panning ponds is caused by not only volatilization of Hg from Au-Hg amalgams, but Hg is also released into the air as dust mixed with dry fine clays, suggesting high long-term environmental risks. Mercury-resistant bacteria associated with clay minerals may have a significant effect on the weathering processes of the ore during long-term bioremediation. The clay mineral complexes on the surface of bacterial cell walls are a stimulator for Hg-resistant bacterial growth in mud ponds contaminated with the Au-Hg materials.     

Calcite and dolomite dissolution rates in the context of microbe–mineral surface interactions

Although microbes have been shown to alter the dissolution rate of carbonate minerals, a mechanistic understanding of the consequences of microbial surface colonization on carbonate dissolution has yet to be achieved. Here we report the use of vertical scanning interferometry (VSI) to study the effect of Shewanella oneidensis MR‐1 surface colonization on the dissolution rates of calcite (CaCO₃) and dolomite (CaMg(CO₃)₂) through qualitative analysis of etch pit development and quantitative measurements of surface‐normal dissolution rates. By quantifying and comparing the significant processes occurring at the microbe–mineral interface, the dominant mechanism of mineral dissolution during surface colonization was determined. MR‐1 attachment under aerobic conditions was found to influence carbonate dissolution through two distinct mechanistic pathways: (1) inhibition of carbonate dissolution through interference with etch pit development and (2) excavation of carbonate material at the cell–mineral interface during irreversible attachment to the mineral surface. The relative importance of these two competing effects was found to vary with the solubility of the carbonate mineral studied. For the faster‐dissolving calcite substrates, inhibition of dissolution by attachment and subsequent extracellular polysaccharide (EPS) production was the dominant effect associated with MR‐1 surface colonization. This interference with etch pit development resulted in a 40–70% decrease in the surface normal dissolution rate relative to cell‐free controls, depending primarily on the concentration of cells in solution. However, in the case of the slower‐dissolving dolomite substrates, carbonate material displaced during the entrenchment of cells on the surface far outweighed the abiotic dissolution rate. Therefore, during the initial stages of surface colonization, dolomite dissolution rates were actually enhanced by MR‐1 attachment. This study demonstrates the dynamic and competitive relationship between microbial surface colonization and mineral dissolution that may be expected to occur in natural environments.     

Scale-dependence and mechanisms of dispersal in freshwater zooplankton

Communities of organisms form as a result of both interspecific and abiotic interactions within local habitat patches and dispersal among patches in a region. Local processes are expected to play a dominant role when dispersal occurs much more often than extinction. We performed two field experiments to examine rates and mechanisms of dispersal in freshwater pond zooplankton communities. First, we tested the effect of distance from a source on the rate of colonization of artificial habitat by placing wading pools at 5, 10, 30 and 60 m from two natural fishless ponds and observing the succession of zooplankton. Seventy-eight percent of the species in the source ponds that were capable of living in the pools colonized at least once during the experiment. A new species was found in the pools on average once every four days, suggesting that colonization events occur on the order of days to weeks for many species. Colonization rates declined further from the source at one pond but not the other, and the effect of distance was relatively weak at both ponds. This suggests that many species disperse broadly over short distances. The second experiment tested the role of animal vectors for zooplankton dispersal by restricting access to the pools. Eight treatments were imposed that excluded potential animal vectors along a body size gradient from large mammals to small insects. While the treatments affected zooplankton colonization, many species invaded even when all animals larger than 1 mm were excluded. Animal vectors may therefore be less important for dispersal than wind. Our results suggest that zooplankton are highly effective dispersers over short distances, and can disperse via several mechanisms. Local interactions should therefore play a dominant role in structuring these communities at small regional scales.     

Colonization of tomato root by pathogenic and nonpathogenic Fusarium oxysporum strains inoculated together and separately into the soil

In soil, fungal colonization of plant roots has been traditionally studied by indirect methods such as microbial isolation that do not enable direct observation of infection sites or of interactions between fungal pathogens and their antagonists. Confocal laser scanning microscopy was used to visualize the colonization of tomato roots in heat-treated soil and to observe the interactions between a nonpathogenic strain, Fo47, and a pathogenic strain, Fol8, inoculated onto tomato roots in soil. When inoculated separately, both fungi colonized the entire root surface, with the exception of the apical zone. When both strains were introduced together, they both colonized the root surface and were observed at the same locations. When Fo47 was introduced at a higher concentration than Fol8, it colonized much of the root surface, but hyphae of Fol8 could still be observed at the same location on the root. There was no exclusion of the pathogenic strain by the presence of the nonpathogenic strain. These results are not consistent with the hypothesis that specific infection sites exist on the root for Fusarium oxysporum and instead support the hypothesis that competition occurs for nutrients rather than for infection sites.     

Anadromous alewives,Alosa pseudoharengus,as prey for white perch,Morone americana

Macroinvertebrates continuously redistribute themselves in the riverbed. A knowledge of the colonization mechanisms and movement patterns is very important for an understanding of processes of restoration of lotic environments, particularly of inland waters with severe pollution. We tested the colonization patterns of stream macroinvertebrates in the Visone River, a tributary of the highly contaminated Bormida River (NW Italy). We placed six groups of traps in the riverbed, each group consisting of three traps: the C trap allowed colonization from all directions, while the D and U traps allowed access only from downstream and upstream respectively. The C traps were the most colonized substrates, both in number of individuals and taxa. The U traps were more colonized than the D traps, demonstrating the great importance of movements directed downstream. We report data on taxonomic and seasonal differences in the colonization process.     

Fate of starch-containing plastic films exposed in aquatic habitats

Plastic films containing cornstarch (40% dry weight) in combination with polyethylene (PE) and polyethylene-co-acrylic acid (EAA) were exposed to river and pond habitats for up to 60 days. Fourier transform infrared (FTIR) spectroscopic analysis of the starch-plastic films indicated that up to about 40% of starch in the films disappeared after 60 days' exposure. PE and EAA components were unchanged during this period. A diverse microbial biofilm quickly accumulated on each of the plastic films in both environments. Although the amount of biofilm accumulation was greater in the river environment than in the pond environment, there was little quantitative difference in the extent of biofilm formation on plastic films composed of PE, EAA, or starch-PE-EAA in either environment. All three types of plastic films were heavily colonized by a midge-fly larva (Dicrotendipes sp.) by 60 days of exposure in the aquatic environments, but only starch-containing plastic films showed any evidence of physical damage that could have been a result of ingestion of the plastic by the larvae (pond>river), suggesting that, in addition to microbial starch degradation, biodisintegration may also be a significant factor influencing the environmental fate of starch-containing plastics.     

Environmental and genetic effects on the formation of ectomycorrhizal and arbuscular mycorrhizal associations in cottonwoods

Although both environment and genetics have been shown to affect the mycorrhizal colonization of host plants, the impacts of these factors on hosts that can be dually colonized by both ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) fungi are less understood. We examined the influence of environment and host crosstype on the EM and AM colonization of cottonwoods (Populus angustifolia and natural hybrids) by comparing levels of colonization of trees growing in common gardens that differed in elevation and soil type. We also conducted a supplemental watering experiment to determine the influence of soil moisture on AM and EM colonization. Three patterns emerged. First, garden location had a significant impact on mycorrhizal colonization, such that EM colonization was 30% higher and AM colonization was 85% lower in the higher elevation garden than the lower elevation garden. Second, crosstype affected total (EM + AM) colonization, but did not affect EM or AM colonization. Similarly, a significant garden × crosstype interaction was found for total colonization, but not for EM or AM colonization. Third, experimental watering resulted in 33% higher EM colonization and 45% lower AM colonization, demonstrating that soil moisture was a major driver of the mycorrhizal differences observed between the gardens. We conclude that environment, particularly soil moisture, has a larger influence on colonization by AM versus EM fungi than host genetics, and suggest that environmental stress may be a major determinant of mycorrhizal colonization in dually colonized host plants.     

Comparison of p-Nitrophenol Biodegradation in Field and Laboratory Test Systems

Acclimation of microbial communities exposed to p-nitrophenol (PNP) was measured in laboratory test systems and in a freshwater pond. Laboratory tests were conducted in shake flasks with water, shake flasks with water and sediment, eco-cores, and two sizes of microcosm. The sediment and water samples used in the laboratory experiments were obtained from the pond. After a 6-day acclimation period, PNP was biodegraded rapidly in the pond. When the pond was treated with PNP a second time, biodegradation began immediately. The acclimation periods in laboratory test systems that contained sediment were similar to that in the pond. The acclimation period was threefold longer in shake flasks without sediment. PNP was biodegraded more slowly by microbial communities acclimated in the laboratory than it was in the pond, and the rate of biodegradation varied with the type of test. The number of bacteria able to mineralize PNP increased by 3 orders of magnitude in the pond during the acclimation period. Similar increases accompanied acclimation in the laboratory systems.     

SUBSTRATUM CONDITIONING AND DIATOM COLONIZATION IN DIFFERENT CURRENT REGIMES1

Short-term (3 day) diatom colonization of clean ceramic tiles and tiles conditioned with a thin, nonalgal biofilm was examined in fast- and slow-current outdoor experimental stream channels to assess effects of organic conditioning and current regime on diatom colonization. Colonization rates onto unconditioned tiles were 10 times lower in fast current that in slow. Substratum conditioning reduced the effects of current because organic conditioning of tiles significantly enhanced colonization in fast current, but not in slow current. Two diatom taxa (Nitzschia acicularis W. Sm. and Synedra radians Kütz) colonized unconditioned tiles more rapidly than conditioned tiles in slow current, suggesting the existence of negative interactions between these diatoms and bacteria and/or organics in conditioning films.     

Colonization of Tomato Root by Pathogenic and Nonpathogenic Fusarium oxysporum Strains Inoculated Together and Separately into the Soil

In soil, fungal colonization of plant roots has been traditionally studied by indirect methods such as microbial isolation that do not enable direct observation of infection sites or of interactions between fungal pathogens and their antagonists. Confocal laser scanning microscopy was used to visualize the colonization of tomato roots in heat-treated soil and to observe the interactions between a nonpathogenic strain, Fo47, and a pathogenic strain, Fol8, inoculated onto tomato roots in soil. When inoculated separately, both fungi colonized the entire root surface, with the exception of the apical zone. When both strains were introduced together, they both colonized the root surface and were observed at the same locations. When Fo47 was introduced at a higher concentration than Fol8, it colonized much of the root surface, but hyphae of Fol8 could still be observed at the same location on the root. There was no exclusion of the pathogenic strain by the presence of the nonpathogenic strain. These results are not consistent with the hypothesis that specific infection sites exist on the root for Fusarium oxysporum and instead support the hypothesis that competition occurs for nutrients rather than for infection sites.     

Prevalence of oral colonization with Candida albicans and anti-C. albicans IgA in the saliva of normal children and children with acute lymphoblastic leukaemia

The prevalence of oral colonization with C. albicans was studied in 40 children with acute lymphoblastic leukaemia (ALL) and 40 matched normal children. Colonization was more common in the ALL group (25% colonized) than the normal group (7.5% colonized). Total saliva IgA levels were lower in the ALL group, but low levels did not correlate with oral colonization. The three normal children with oral colonization all had anti-C. albicans IgA in their saliva, as had seven of the ten colonized ALL patients.