Behavior,activities, and effects of bacteria on synthetic quartz monocrystal surfaces

Two strains ofBacillus sp. and a strain ofBrevibacterium sp., originally isolated from a natural quartzite surface, were characterized and employed as test strains with several methods: acridine orange fluorochromation and epifluorescence microscopy were used for detection of individual cells; scanning and transmission microscopy for studying attachment behavior; replica techniques in combination with electron microscopy for following surface interaction effects; and chemical analysis of SiO₂ for detecting possible silica leaching activities. The experimental results clearly showed that the three test strains were able to attach to and grow on the precleaned quartz surfaces. Attachment modes were either by direct sorption mechanisms (Brevibacterium sp. S) or the production of adhesive polymers (Bacillus sp. U andBacillus sp. W). In short-term contact incubation experiments with rich media, neither quartz crystal surface structures nor bacterial cell surfaces appeared to be changed. Likewise, significant biochemical dissolution and mechanical dislocation of SiO₂ (which would have indicated rapid bacterial weathering activities) could not be detected. The importance of quartz purity and crystalline structure for the initiation of weathering processes is discussed.     

Desiccation independence of terrestrialNostoc commune ecotypes (cyanobacteria)

The subspeciesNostoc commune var.flagelliforme andN. commune var.commune are found in China (Ningxia Province, Inner Mongolia) as two morphologically different ecotypes of the desiccation-independent cyanobacteriumN. commune. The first ecotype, but not the second, colonizes arid areas. Various biochemical parameters and water dependence of photosynthesis and nitrogen fixation were compared for both ecotypes. Different patterns of water stress proteins were found in the two ecotypes. Repeated desiccation resulted in an enhanced desiccation independence for photosynthesis and, in the case of the ecotypecommune, for nitrogen fixation. The different response of nitrogenase of both ecotypes towards repeated cycles of rewetting and desiccation under conditions simulating the natural environment is discussed in terms of the energy balance of the colonies that are adapted to different environmental conditions.     

Modern and fossil traces in terrestrial lithic substrates

A number of biogenic processes leads to the formation of distinctive traces in terrestrial lithic substrates. These include: burrowing by vertebrates in moderately lithified rocks; scraping by mammals; smoothing and polishing of limestone surfaces by the locomotion of mammals; excavation by bees, wasps, and ants producing nesting and dwelling tunnels; dissolution of limestone surfaces by terrestrial snails; endolithic activity of fungi, algae, and lichens on subaerial rock surfaces; root corrosion; etc. Processes of biochemical weathering, biophysical erosion, and enlargement of cracks and fissures by the pressure of plant roots do not leave distinctive traces and therefore lie outside the ichnological realm. The fossil preservation of terrestrial bioerosional traces is expected to be uncommon. Nevertheless, various possible means of preservation must be considered, such as by rapid burial by volcanic material, by fluvial sediments, by travertine or tufa, by loess, “conservation”; in caves, case hardening of surfaces of porous rocks, and preservation of subsoil traces below fossil soils.     

Further Readings in Geomicrobiology

Microbial biofilms preferentially colonized pyrite surfaces of black shale incubated in groundwater in the Newark Basin (northeastern United States) for 1 month. SEM observation revealed the co-occurrence of bacteria-shaped pits and secondary iron minerals on pyrite, which indicate biological involvement in pyrite weathering and secondary solid formation. Of the 24 16S rDNA sequences obtained from bacterial communities on pyrite, arsenopyrite and quartz sand, 22 belonged to the phylum proteobacteria, including 5 identified as β or ?-proteobacteria capable of oxidizing iron or sulfur, 16 identified as members of the Fe(III)-reducing Geobacteraceae in the δ-proteobacteria and one identified as the Fe(III)-reducing Ferribacterium. Results indicate that microbes play an essential role in the oxidation of iron sulfides (via direct contact and indirect pathways) and the reduction of iron oxides in pyrite-bearing substrata of a slightly acidic black shale aquifer.     

The effect of rock composition on cyanobacterial weathering of crystalline basalt and rhyolite

The weathering of volcanic rocks contributes significantly to the global silicate weathering budget, effecting carbon dioxide drawdown and long‐term climate control. The rate of chemical weathering is influenced by the composition of the rock. Rock‐dwelling micro‐organisms are known to play a role in changing the rate of weathering reactions; however, the influence of rock composition on bio‐weathering is unknown. Cyanobacteria are known to be a ubiquitous surface taxon in volcanic rocks. In this study, we used a selection of fast and slow growing cyanobacterial species to compare microbial‐mediated weathering of bulk crystalline rocks of basaltic and rhyolitic composition, under batch conditions. Cyanobacterial growth caused an increase in the pH of the medium and an acceleration of rock dissolution compared to the abiotic controls. For example, Anabaena cylindrica increased the linear release rate () of Ca, Mg, Si and K from the basalt by more than fivefold (5.21–12.48) and increased the pH of the medium by 1.9 units. Although A. cylindrica enhanced rhyolite weathering, the increase in was less than threefold (2.04–2.97) and the pH increase was only 0.83 units. The values obtained with A. cylindrica were at least ninefold greater with the basalt than the rhyolite, whereas in the abiotic controls, the difference was less than fivefold. Factors accounting for the slower rate of rhyolite weathering and lower biomass achieved are likely to include the higher content of quartz, which has a low rate of weathering and lower concentrations of bio‐essential elements, such as, Ca, Fe and Mg, which are known to be important in controlling cyanobacterial growth. We show that at conditions where weathering is favoured, biota can enhance the difference between low and high Si‐rock weathering. Our data show that cyanobacteria can play a significant role in enhancing rock weathering and likely have done since they evolved on the early Earth.     

Occurrence of the Root Rot Pathogen,Fusarium commune,in Forest Nurseries of?the Midwestern and Western United States

Fusarium commune can cause damping‐off and root rot of conifer seedlings in forest nurseries, and this pathogen has been previously reported from Oregon, Idaho, and Washington, USA. We collected Fusarium isolates from additional nurseries in the midwestern and western USA to more fully determine occurrence of this pathogen. We used DNA sequences of the mitochondrial small subunit gene to identify F. commune. In addition to confirming the occurrence of F. commune in Oregon, Idaho, and Washington, USA, we also discovered that F. commune is even more widespread with this first report of F. commune occurring in Nevada, Montana, Nebraska, and Michigan, USA.     

An RNA-Sequencing Study of the Genes and Metabolic Pathways Involved in Aspergillus niger Weathering of Potassium Feldspar

Microbial transformation of potassium feldspar to produce organic composite potassium fertilizer is recognized to be an important method of effective use of the huge reserves of low grade K⁺-bearing rock in China. The mechanism underlying microbial weathering of silicate minerals is still unclear, and this is an obstacle to practical methods of application. To thoroughly understand the molecular mechanism responsible for the weathering of potassium feldspar by Aspergillus niger at a molecular level, high-throughput RNA-sequencing (RNA-seq) and treatment with different potassium sources (cultured in Czapek medium with soluble K⁺ or potassium feldspar) were used to investigate the differentially expressed genes of A. niger associated with potassium feldspar weathering and the related metabolic pathways. A series of differentially expressed genes related to the synthesis and transportation of organic acids, polysaccharides, and proteins (enzymes) were found to be closely associated with the K⁺ released from minerals through bioinformatic analysis. In addition, 12 genes that showed apparent expression differences by RNA-seq analysis and are relevant to organic acid synthesis, protein modification, maintenance of cellular homeostasis, and material transportation, were selected to be further verified using RT-qPCR. Compared to the fungal samples cultured with soluble K⁺, those with potassium feldspar have certain genes that are more up-regulated, such as the genes for Na⁺,K⁺-ATPase (447.6 multiples), cystathionine beta-synthase (5.6 multiples), cysteine synthase (9 multiples), and glutathione synthase (3.5 multiples). The analysis indicates that A. niger weathering of potassium feldspar is due to the synergistic effect of many factors including the up-regulation of certain genes and activation of related metabolite pathways. The research improves our understanding of the mechanisms of microbial weathering of silicate minerals.     

Four chemotypes of the terrestrial cyanobacterium Nostoc commune characterized by differences in the mycosporine‐like amino acids

The cyanobacterium Nostoc commune is adapted to terrestrial environments and has a cosmopolitan distribution. Four genotypes of N. commune can be identified based on differences in their 16S rRNA genes, and these genotypes are distributed throughout Japan without regional specificity. Mycosporine‐like amino acids (MAAs) are UV‐absorbing pigments, and novel glycosylated MAA derivatives with radical scavenging activities have been identified in N. commune. In this study, we investigated the consistency of the relationship between MAA compositions and N. commune genotypes. The MAA compositions were different in a genotype‐specific manner, suggesting that the types of MAA derivatives can feasibly be used as chemotaxonomic markers to characterize N. commune. The novel 756‐Da MAA, which was identified as an aglycone of the 1050‐Da MAA and named nostoc‐756, occurred in genotype C of N. commune. Nostoc‐756 functioned as a radical scavenger in vitro. In conclusion, N. commune is classified into four groups representing genetically different chemotypes, namely, the arabinose‐bound porphyra‐334 producer (chemotype A), the glycosylated nostoc‐756 producer (chemotype B), the nostoc‐756 producer (chemotype C) and the glycosylated palythine‐threonine producer (chemotype D). Either the molecular taxonomical method or chemical analysis of a characteristic secondary metabolite is sufficient to identify the types of N. commune; however, there are no obvious ecophysiological differences that allow us to distinguish them.     

Bottom‐up effects of lake sediment on pelagic food‐web compartments: a mesocosm study

相似文献   

Features of the reproductive ecology of the rock catfish Silurus lithophilus

Some aspects of the reproductive ecology of the rock catfish Silurus lithophilus (Siluriformes: Siluridae), a species endemic to the Lake Biwa system, were investigated from April to July in 1989–1994. Field observations were conducted at a rocky shoal, which was also a spawning ground of S. biwaensis, along the shore of the Seta River, the lake's outlet. Spawning of S. lithophilus occurred around midnight at shallow, rocky places on the shoal (5–70 cm in water depth) from early May to mid-July, starting earlier than S. biwaensis (mid-May to mid-July). Spawning tended to occur at low water temperatures irrespective of high-water events, unlike S. biwaensis, and in low densities (fewer than 8 fish per night) compared to S. biwaensis (1–45 fish per night). Although the rock catfish tended to appear and spawn at higher frequencies on nights when S. biwaensis spawned or appeared, it always avoided conflict with the latter species by spawning at sites far from those used by S. biwaensis or after S. biwaensis had left the vicinity. The survival of eggs of S. lithophilus might be favored by a strategy of diverting predator attention from them by synchronizing spawning nights with S. biwaensis. Received: February 27, 2001 / Revised: October 17, 2001 / Accepted: November 8, 2001     

Decolorization of effluent from the bagasse-based pulp mills by white-rot fungus,Schizophyllum commune

Summary The effluent from bagasse-based pulp and paper mills can be decolorized with the white-rot fungus Schizophyllum commune. The influence of pH, nutrients and aeration on the decolorizing efficiency of this fungus has been determined. It was found that it could not degrade lignin unless a more easily metabolized carbon source was made available simultaneously. The addition of carbon and nitrogen not only improved the decolorizing efficiency of the fungus, but also resulted in reduction of the biological oxygen demand (BOD) and chemical oxygen demand (COD) of effluent. A 2-day incubation period was sufficient for lignin breakdown by S. commune. The efficiency of treatment of effluent with this fungus was highest at pH 4–5 and was further improved by intermittent aeration.     

Environmental hazards of arsenic associated with black shales: a review on geochemistry, enrichment and leaching mechanism

Black shales are high organic matter-rich dark coloured mudstones those are often deposited during ??oceanic anoxia events??. Most of the black shale horizons are rich in arsenic far above their average crustal abundance and are susceptible to weathering eventually leaching high As contents to the surrounding environment causing As enrichment in soil and water which adversely affect the living beings. Numerous arsenic contaminations are being reported from black shale hosted areas globally, hence, making extremely crucial to understand the processes of enrichment, leaching and broader prospective of environmental hazards. Few studies have shown arsenic concentrations as high as 6,000?mg/kg within black shales causing groundwater enrichment up to hundreds mg/L. Arsenic is commonly attached to sulphide mineral structure and partly to organic matter and clay contents during deposition and diagenetic processes. Majority of sulphide bound arsenic becomes available to oxidative dissolution processes in presence of atmospheric oxygen and water which is further triggered by certain microbial community such as Acidophilus ferrooxidans hence, enhancing arsenic release. Physical weathering processes carry the arsenic-rich shale constituents to the depositional site where it is dissolved subsequently. Chemical diffusion and mechanical transport are two prime processes transporting arsenic from black shale horizons to the water bodies or soil columns, while air pollutions are caused by combustions of organic matter-rich coaly shales.     

First discovery of Stephanus Jurine (Hymenoptera: Stephanidae) in Japan,with description of a new species from Anijima Island of Ogasawara Islands

The genus Stephanus Jurine (in Panzer) is newly recorded from Japan and is represented by a new species. S. anijimensis sp. nov. from Anijima Island of the Ogasawara Islands. This species resembles S. tridentatus van Achterberg & Yang from the Oriental part of China, but can be distinguished by the combination of following characters: pronotum with a cavity under pronotal fold (cavity absent in S. tridentatus); hind femur comparatively slender, 4.8–5.1 times as long as maximum width (about 4.1 times in S. tridentatus); apical 0.5 of hind femur black or blackish‐brown (more or less yellowish in S. tridentatus). This new species was not found from other islands of the Ogasawara Islands, in which fauna is being severely endangered mainly due to predation by the introduced green anoles. Recently, it was introduced into Anijima Island in March 2013 and thus the extinction risk of this species is very high on this island.     

Studies of some biochemical and physicochemical properties of an inducible form of extracellular laccase from the basidiomyceteCoriolus hirsutus

An inducible form of extracellular laccase (EC 1.14.18.1) was isolated from the basidiomyceteCoriolus hirsutus. The induction was performed with 0.11 μM syringaldazine, a substrate of laccase. The inducible form of the enzyme consisted of two isoforms, laccase II and laccase 12, whose molecular weights were 69 ±2 and 67 ±2 kDa, respectively. The isoelectric points of these isoenzymes were found to be 3.5 and 4.2, respectively. The optimum pH range for both laccases was 4.4–4.6, and the optimum temperature was 50°C. The thermal stability of these isoenzymes was examined, andK _m values for the substrates syringaldazine and pyrocatechol were determined. Our biochemical and physicochemical studies demonstrated that inducible laccase isoforms differed from constitutive forms in molecular weight, IEP,K _m, and thermal stability. However, their optimum pH ranges and temperatures were identical.     

柳杉种植对黔西南喀斯特山区金发藓沼泽植物群落和储水功能的影响

藓类沼泽对喀斯特山区生物多样性维持和水源涵养有重要作用,需加强人工林种植对喀斯特山区藓类沼泽生态功能影响的研究。以黔西南典型金发藓沼泽为研究对象,分析了人工柳杉林对林下金发藓植物群落和金发藓沼泽储水功能的影响。主要研究结果为：1）柳杉种植对金发藓植物群落有负面影响。随柳杉密度增加,林下金发藓植物群落的盖度、平均高度和物种多样性显著下降;2）表层土壤含水量是金发藓沼泽储水量的主要贡献者。柳杉种植显著提高了干季表层土壤的含水量,但高密度柳杉林显著降低了雨季表层土壤的含水量;柳杉种植未对干季金发藓含水量造成影响,低密度柳杉林显著提高了雨季金发藓植物的含水量;3）柳杉密度对金发藓沼泽生态系统储水量的影响存在明显季节差异：在雨季呈负影响,在干季呈正影响;4）柳杉种植有利于维持金发藓沼泽储水能力的稳定性,尤其是当柳杉密度较低时这种效果更明显。表明人工柳杉林对金发藓沼泽的影响是非线性的,合适密度的柳杉种植可提升金发藓沼泽的储水能力。     

Lipase in aqueous‐polar organic solvents: Activity,structure, and stability

Studying alterations in biophysical and biochemical behavior of enzymes in the presence of organic solvents and the underlying cause(s) has important implications in biotechnology. We investigated the effects of aqueous solutions of polar organic solvents on ester hydrolytic activity, structure and stability of a lipase. Relative activity of the lipase monotonically decreased with increasing concentration of acetone, acetonitrile, and DMF but increased at lower concentrations (upto ～20% v/v) of dimethylsulfoxide, isopropanol, and methanol. None of the organic solvents caused any appreciable structural change as evident from circular dichorism and NMR studies, thus do not support any significant role of enzyme denaturation in activity change. Change in 2D [15N, 1H]‐HSQC chemical shifts suggested that all the organic solvents preferentially localize to a hydrophobic patch in the active‐site vicinity and no chemical shift perturbation was observed for residues present in protein's core. This suggests that activity alteration might be directly linked to change in active site environment only. All organic solvents decreased the apparent binding of substrate to the enzyme (increased K_m); however significantly enhanced the k_cat. Melting temperature (T_m) of lipase, measured by circular dichroism and differential scanning calorimetry, altered in all solvents, albeit to a variable extent. Interestingly, although the effect of all organic solvents on various properties on lipase is qualitatively similar, our study suggest that magnitudes of effects do not appear to follow bulk solvent properties like polarity and the solvent effects are apparently dictated by specific and local interactions of solvent molecule(s) with the protein.     

Rewetting of drought-resistant blue-green algae: Time course of water uptake and reappearance of respiration,photosynthesis, and nitrogen fixation

Summary The response of the terrestrial blue-green algae Nostoc flagelliforme, Nostoc commune, and Nostoc spec. to water uptake has been investigated after a drought period of approximately 2 years. Rapid half-times of rewetting (0.6, 3.3, and 15.5 min, respectively) are found. The surfaceto-mass ratio of the three species is inversely correlated to the speed of water uptake and loss. The ecological relevance of these different time courses is discussed.Respiration starts immediately after a 30-min rewetting period, whereas photosynthetic oxygen evolution reaches its maximum activity after 6 and 8 h with N. commune and N. flagelliforme, respectively. In the dark, recovery of oxygen uptake by N. commune is somewhat impaired, while slightly stimulated with N. flagelliforme. With both species, recovery of photosynthesis is inhibited by darkness.Using colonies kept dry for two years, nitrogenase activity of N. commune attains its maximum 120 to 150 h after rewetting, while only 50 h were needed with algal mats kept dry for two days.Thus, after a 2-year drought period, the physiological sequence of reactivation is respiration—photosynthesis—nitrogen fixation. Respiration and photosynthesis precede growth and are exhibited by existing vegetative cells, whereas recovery of nitrogen fixation is dependent on newly differentiated heterocysts.     

Impact of inorganic salts on degradation of bisphenol A and diclofenac by crude extracellular enzyme from Pleurotus ostreatus

This study investigated the influence of inorganic salts on enzymatic activity and the removal of trace organic contaminants (TrOCs) by crude laccase from the white-rot fungus Pleurotus ostreatus. A systematic analysis of 15 cations and anions from common inorganic salts was presented. Laccase activity was not inhibited by monovalent cations (i.e. Na⁺, NH₄⁺, K⁺), while the presence of divalent and trivalent cations showed variable impact – from negligible to complete inhibition – of both laccase activity and its TrOC removal performance. Of interest was the observation of discrepancy between residual laccase activity and TrOC removal in the presence of some ions. Mg²⁺ had negligible impact on residual laccase activity but significant impact on TrOC removal. Conversely, F^? showed greater impact on residual laccase activity than on TrOC removal. This observation indicated different impacts of the interfering ions on the interaction between laccase and TrOCs as compared to that between laccase and the reagent used to measure its activity, implicating that residual laccase activity may not always be an accurate indicator of TrOC removal. The degree of impact of halides was in the order of F^??>?I^? >?Br^??>?Cl^?. Particularly, the tolerance of the tested laccase to Cl^? has important implications for a range of industrial applications.     

Effect of growth substrate,method of fermentation,and nitrogen source on lignocellulose-degrading enzymes production by white-rot basidiomycetes

The exploration of seven physiologically different white rot fungi potential to produce cellulase, xylanase, laccase, and manganese peroxidase (MnP) showed that the enzyme yield and their ratio in enzyme preparations significantly depends on the fungus species, lignocellulosic growth substrate, and cultivation method. The fruit residues were appropriate growth substrates for the production of hydrolytic enzymes and laccase. The highest endoglucanase (111 U ml⁻¹) and xylanase (135 U ml⁻¹) activities were revealed in submerged fermentation (SF) of banana peels by Pycnoporus coccineus. In the same cultivation conditions Cerrena maxima accumulated the highest level of laccase activity (7,620 U l⁻¹). The lignified materials (wheat straw and tree leaves) appeared to be appropriate for the MnP secretion by majority basidiomycetes. With few exceptions, SF favored to hydrolases and laccase production by fungi tested whereas SSF was appropriate for the MnP accumulation. Thus, the Coriolopsis polyzona hydrolases activity increased more than threefold, while laccase yield increased 15-fold when tree leaves were undergone to SF instead SSF. The supplementation of nitrogen to the control medium seemed to have a negative effect on all enzyme production in SSF of wheat straw and tree leaves by Pleurotus ostreatus. In SF peptone and ammonium containing salts significantly increased C. polyzona and Trametes versicolor hydrolases and laccase yields. However, in most cases the supplementation of media with additional nitrogen lowered the fungi specific enzyme activities. Especially strong repression of T. versicolor MnP production was revealed.