Abundance, biomass, structure, and activity of the microbial complexes of minerotrophic and ombrotrophic peatlands

Very large microbial biomass was revealed in peat bogs by means of fluorescence microscopy. In ombrotrophic peatlands, the pool of the dry-weight microbial biomass in the 1.5-m layer constituted 3-4 t/ha and was twice as high as in the minerotrophic peat bogs. Fungal biomass was predominant (55-99%) in ombrotrophic peatlands, while bacterial biomass predominated in minerotrophic peatlands (55-86%). In ombrotrophic peatlands, the microbial biomass was concentrated in the upper layers, while in minerotrophic peatlands, it was uniformly distributed in the bulk. After drainage, the microbial pool in the ombrotrophic peatlands increased twofold; that in the minerotrophic peatlands remained at the same level. The potential activity of nitrogen fixation and denitrification was revealed across the whole profile of the peatlands. The average values of these potential activities were five times higher in the minerotrophic peatlands, where bacterial biomass predominated.     

Abundance,biomass, structure,and activity of the microbial complexes of minerotrophic and ombrotrophic peatlands

A very large microbial biomass was revealed in peat bogs by means of fluorescence microscopy. In ombrotrophic peatlands, the pool of the dry-weight microbial biomass in the 1.5-m layer constituted 3–4 t/ha and was twice as high as in the minerotrophic peat bogs. Fungal biomass was predominant (55–99%) in ombrotrophic peatlands, while bacterial biomass predominated (55–86%) in minerotrophic peatlands. In ombrotrophic peatlands, the microbial biomass was concentrated in the upper layers, while in minerotrophic peatlands, it was uniformly distributed in the bulk. After drainage, the microbial pool in the ombrotrophic peatlands increased twofold; that in the minerotrophic peatlands remained at the same level. The potential activity of nitrogen fixation and denitrification was revealed across the whole profile of the peatlands. The average values of these potential activities were five times higher in the minerotrophic peatlands, where bacterial biomass predominated.     

环境微生物群落结构与功能多样性研究方法

微生物群落的结构及群落内种间相互作用是影响其生态功能的决定性因素。尽管微生物群落是地球生物化学循环的主要驱动者,但是由于传统的微生物培养方法只能分离约1%10%的环境微生物,对复杂的环境微生物群落结构和功能多样性了解甚少。元基因组学、单细胞分析和群落遗传学等方法的出现,及其与微生物学的交叉融合,使得人们能够从微生物群落组成、物种功能、种间相互作用和预测模型等方面分析微生物群落。重点综述了元基因组学、单细胞分析和群落遗传学等方法及其在环境微生物群落结构和功能多样性中的应用进展。     

Distribution of microbial populations and their relationship with environmental parameters in the coastal waters of Qingdao,China

In order to understand the large‐scale distribution of microbial populations simultaneously and their relationship with environmental parameters, flow cytometry was used to analyse samples collected from 46 stations in the coastal waters of Qingdao in spring, 2007. The distribution of virus was significantly and positively correlated with heterotrophic bacteria. Two groups of picophytoplankton (Synechococcus and picoeukaryotes) were detected; however, Prochlorococcus was not found. Picoeukaryotes and nanophytoplankton were abundant in the near‐shore waters, whereas Synechococcus was abundant in the off‐shore areas. No variation was found in vertical distribution of virus, heterotrophic bacteria, Synechococcus and nanophytoplankton abundances, except picoeukaryotes abundance in the bottom layer was dramatically lower than that in the upper layers. Correlation analyses indicated that the relationship between abiotic variables and heterotrophic bacteria, pico‐ and nanophytoplankton was closer than that between abiotic variables and virioplankton. Temperature and nutrients were the synchronous factors controlling the growth of heterotrophic bacteria, pico‐ and nanophytoplankton in the coastal waters of Qingdao in spring. The results suggested that synergistic and antagonistic effects existed among microbial groups.     

Stratification and dynamics of microbial loop communities in Lake Fryxell, Antarctica

1. Lake Fryxell, situated in the McMurdo Dry Valleys, Antarctica, offers the opportunity to study microbial loop processes in the absence of crustacean zooplankton and other higher organisms. This is the first study of Lake Fryxell to provide detailed temporal and vertical variations of microbial loop organisms.
2. Protozoan communities are concentrated around the chemocline (9–10 m) in Lake Fryxell. Phototrophic nanoflagellates (PNAN), heterotrophic nanoflagellates (HNAN) and ciliates formed deep maxima of 14 580, 694 and 58 cells mL−1 respectively. Although abundance and biomass at the chemocline was high, diversity of protozoa was low, Plagiocampa accounting for> 80% of the total ciliate biomass.
3. In the mixolimnion (4.5–8 m), protozoa were less abundant, but more diverse, with 24 ciliate morphotypes being identified within this region of the water column. Inter-annual variability of protozoan biomass and abundance was greater in the mixolimnion than at the chemocline due to more variable nutrient and prey concentrations.
4. Physicochemical gradients in Lake Fryxell were very stable because the perennial ice cover reduced wind driven currents. As a consequence, ciliate species occurred in distinct depth strata, Monodinium being most abundant directly beneath the ice cover, Askenasia having maximum abundance at 8 m and Plagiocampa dominating ciliate biomass at the chemocline. The lack of vertical mixing reduced seasonal successions of PNAN and ciliate species. Three cryptophyte species dominated the PNAN community at all times (>79% of total biomass).     

Seasonal dynamics in the community structure and trophic structure of testate amoebae inhabiting the Sanjiang peatlands,Northeast China

Peatlands cover 3% of the earth’s land surface but contain 30% of the world’s soil carbon pool. Microbial communities constitute a crucial detrital food web for nutrient and carbon cycling in peatlands. Heterotrophic protozoans are considered top predators in the microbial food web; however, they are not yet well understood. In this study, we investigated seasonal dynamics in the community and the trophic structure of testate amoebae in four peatlands. Testate amoebae density and biomass in August were significantly higher than those in May and October. The highest density, 6.7 × 10⁴ individual g⁻¹ dry moss, was recorded in August 2014. The highest biomass, 7.7 × 10² μg C g⁻¹ dry moss, was recorded in August 2013. Redundancy analyses showed that water-table depth was the most important factor, explaining over one third of the variance in fauna communities in all sampled seasons. High trophic position taxa dominated testate amoebae communities. The Shannon diversity index and community size structure index declined from August to October in 2013 and from May to October in 2014. These seasonal patterns of testate amoebae indicated the seasonal variations of the peatlands’ microbial food web and are possibly related to the seasonal carbon dynamics in Northeast Chinese peatlands.     

Water and bacteriorhodopsin: structure, dynamics, and function

A wealth of information has been gathered during the past decades that water molecules do play an important role in the structure, dynamics, and function of bacteriorhodopsin (bR) and purple membrane. Light-induced structural alterations in bR as detected by X-ray and neutron diffraction at low and high resolution are discussed in relationship to the mechanism of proton pumping. The analysis of high resolution intermediate structures revealed photon-induced rearrangements of water molecules and hydrogen bonds concomitant with conformational changes in the chromophore and the protein. These observations led to an understanding of key features of the pumping mechanism, especially the vectoriality and the different modes of proton translocation in the proton release and uptake domain of bR. In addition, water molecules influence the function of bR via equilibrium fluctuations, which must occur with adequate amplitude so that energy barriers between conformational states can be overcome.     

Anticodon loop of tRNAPhe: structure, dynamics, and Mg2+ binding

The structure, dynamics, and Mg2+ binding reactions of the isolated anticodon hairpin loop from tRNAPhe (yeast) have been analyzed by fluorescence-detected temperature-jump relaxation, melting experiments, and equilibrium sedimentation. Most of the measurements were performed at an ionic strength of 0.15 M and at temperatures below 25 degrees C, where the hairpin loop proved to be stable. A relaxation effect with a time constant of approximately 100 microseconds, indicated by the Wye base fluorescence, is attributed to a conformational change of the anticodon loop and is very similar to a corresponding transition observed previously for the whole tRNAPhe molecule. A Mg2+ binding site reflected by an inner-sphere relaxation process and associated with a strong increase of the Wye base fluorescence closely resembles a corresponding site observed in the complete tRNAPhe and is attributed to a site in the anticodon loop identified by X-ray analysis. In addition to the Mg2+ site in the loop, which is associated with a binding constant of 2 X 10(3) M-1, the existence of sites with a higher affinity is demonstrated by an unusual relaxation effect, showing a minimum in the reciprocal time constant with increasing Mg2+ concentration. The experimental data can be described by a transition between two states and Mg2+ binding to both states resulting in a reaction cycle, which is extended by an additional Mg2+ binding reaction to one of the states. The unusual effect has not been observed for the complete tRNAPhe and is also not observed when Ca2+ is added instead of Mg2+. This result indicates the existence of a conformational change involving Mg2+ inner-sphere complexation.(ABSTRACT TRUNCATED AT 250 WORDS)     

冻融循环对金川泥炭沼泽土壤微生物量及群落结构的影响

冻融作用显著改变土壤微生物活性及碳氮循环过程。以长白山金川泥炭沼泽0-15 cm和15-30 cm土壤为研究对象,进行室内冻融交替模拟实验。实验设置两个冻融幅度（-10-10℃和-5-5℃）。经过0/1/3/5/7/15次冻融循环后,分别采用氯仿熏蒸法和磷脂脂肪酸法测定泥炭沼泽土壤微生物量及磷脂脂肪酸含量,并与未进行冻融处理的FTC （0）对比。实验结果表明：冻融作用对土壤微生物量碳、氮及微生物磷脂脂肪酸含量有显著影响（P<0.001）。15次冻融交替作用后,土壤微生物碳（MBC）含量均显著增加,土壤微生物量氮（MBN）含量显著降低。两种冻融模式下,各类型微生物磷脂脂肪酸含量均显著降低。冻融作用显著改变了泥炭沼泽土壤微生物群落结构。冻融作用降低了土壤真菌/细菌比值（-5-5℃,0-15 cm土壤除外）,增加了革兰氏阳性菌/革兰氏阴性菌比值。-5-5℃冻融作用下,各土壤微生物磷脂脂肪酸含量变幅大于-10-10℃,土壤MBC的变化则与其相反,在-10-10℃变化幅度更大。两种冻融幅度下MBC与大部分微生物群落在15-30 cm土壤的变幅更大,这说明冻融作用对不同深度土壤微生物量和微生物群落结构的影响存在差异。冻融次数对土壤微生物量和各类型磷脂脂肪酸含量有显著影响（P<0.01）。相关性分析结果表明多种微生物磷脂脂肪酸含量与MBN含量呈正相关关系（P<0.01）,与DOC含量呈负相关关系（P<0.05）。综上,冻结作用促进了微生物的死亡,为融化期微生物生存提供更多碳源与营养物质,改变了土壤微生物群落结构。冻融期间各类型微生物磷脂脂肪酸含量降低,可能会降低泥炭沼泽土壤碳汇能力。     

Review: the dynamics of the nuclear lamins during the cell cycle-- relationship between structure and function

The nuclear lamins are members of the intermediate filament (IF) family of proteins. The lamins have an essential role in maintaining nuclear integrity, as do the other IF family members in the cytoplasm. Also like cytoplasmic IFs, the organization of lamins is dynamic. The lamins are found not only at the nuclear periphery but also in the interior of the nucleus, as distinct nucleoplasmic foci and possibly as a network throughout the nucleus. Nuclear processes such as DNA replication may be organized around these structures. In this review, we discuss changes in the structure and organization of the nuclear lamins during the cell cycle and during cell differentiation. These changes are correlated with changes in nuclear structure and function. For example, the interactions of lamins with chromatin and nuclear envelope components occur very early during nuclear assembly following mitosis. During S-phase, the lamins colocalize with markers of DNA replication, and proper lamin organization must be maintained for replication to proceed. When cells differentiate, the expression pattern of lamin isotypes changes. In addition, changes in lamin organization and expression patterns accompany the nuclear alterations observed in transformed cells. These lamin structures may modulate nuclear function in each of these processes.     

Immunoglobulin superfamily: structure, function and relationship to other receptor molecules.

The immunoglobulin superfamily includes the most diverse group of receptors known. They are united by the possession of a common structural feature, the immunoglobulin homology domain. They are found in species from insects to man. They are central to both the humoral and cell mediated immune reactions; they serve as cell surface receptors responsible for positional ques during embryonic development, as well as viral and growth factor receptors. They function in conjunction with other receptor families including the integrins and selectins. Thus, they are frequently parts of adhesive cascades and as such activate signal transducing systems required for the expression or activation of other cell surface receptors. They continue to be the targets of intense investigation into the molecular basis of adhesive interactions.     

The impact of environmental perturbation on microbial community structure and dynamics: Factors affecting growth of Clonothrix fusca in groundwater

Abstract

In a previous work temporal succession of two sheathed, filamentous methanotrophic γ-Proteobacteria, Crenothrix polyspora and Clonothrix fusca, was observed by analyzing the microbial community of an artesian well. Although a correlation between physical-chemical environmental parameters and growth of these microorganisms was suggested, the link with the microbial physiology remained elusive. In this study we demonstrate that phosphatidylethanolamine and cardiolipin, generally abundant in most γ-Proteobacteria, could not be detected in C. fusca membranes by thin-layer chromatography. The absence of cardiolipin was supported by results of enzymatic assay of cardiolipin synthase activity and by Southern blot analysis that failed to detect cls homologous sequences in the genomic DNA of this microorganism. The absence of phosphatidylethanolamine and cardiolipin might account for requirement of millimolar concentrations of magnesium and calcium for growth, and for massive over-growth of this microorganism during the winter season when the water levels of magnesium and calcium increased in the artesian well.     

Inorganic nutrients,bacteria, and the microbial loop

The realization that natural assemblages of planktonic bacteria may acquire a significant fraction of their nitrogen and phosphorus via the uptake of dissolved inorganic nutrients has modified our traditional view of these microorganisms as nutrient remineralizers in plankton communities. Bacterial uptake of inorganic nitrogen and phosphorus may place bacteria and phytoplankton in competition for growth-limiting nutrients, rather than in their traditional roles as the respective source and sink for these nutrients in the plankton. Bacterial nutrient uptake also implies that bacterivorous protozoa may play a pivotal role in the remineralization of these elements in the microbial loop. The overall contribution of bacterial utilization of inorganic nutrients to total nutrient uptake in the ocean is still poorly understood, but some generalizations are emerging with respect to the geographical areas and community physiological conditions that might elicit this behavior.     

Enzymes: An integrated view of structure, dynamics and function

Microbes utilize enzymes to perform a variety of functions. Enzymes are biocatalysts working as highly efficient machines at the molecular level. In the past, enzymes have been viewed as static entities and their function has been explained on the basis of direct structural interactions between the enzyme and the substrate. A variety of experimental and computational techniques, however, continue to reveal that proteins are dynamically active machines, with various parts exhibiting internal motions at a wide range of time-scales. Increasing evidence also indicates that these internal protein motions play a role in promoting protein function such as enzyme catalysis. Moreover, the thermodynamical fluctuations of the solvent, surrounding the protein, have an impact on internal protein motions and, therefore, on enzyme function. In this review, we describe recent biochemical and theoretical investigations of internal protein dynamics linked to enzyme catalysis. In the enzyme cyclophilin A, investigations have lead to the discovery of a network of protein vibrations promoting catalysis. Cyclophilin A catalyzes peptidyl-prolyl cis/trans isomerization in a variety of peptide and protein substrates. Recent studies of cyclophilin A are discussed in detail and other enzymes (dihydrofolate reductase and liver alcohol dehydrogenase) where similar discoveries have been reported are also briefly discussed. The detailed characterization of the discovered networks indicates that protein dynamics plays a role in rate-enhancement achieved by enzymes. An integrated view of enzyme structure, dynamics and function have wide implications in understanding allosteric and co-operative effects, as well as protein engineering of more efficient enzymes and novel drug design.     

Supramolecular glycopolymers: How carbohydrates matter in structure,dynamics, and function

Supramolecular glycopolymers exhibiting inherent dynamicity, tunability, and adaptivity allow us to arrive at a deeper understanding of multivalent carbohydrate–carbohydrate interactions and carbohydrate–protein interactions, both being essential to key biological events. The impacts of the carbohydrate segments in these supramolecular glycopolymers towards their structure, dynamics, and function as biomaterials are addressed in this minireview. Bottlenecks and challenges are discussed, and we speculate about possible future directions.     

Structure and function in the euglenoid eyespot apparatus: The fine structure,and response to environmental changes

Summary The microanatomy of the eyespot apparatus of Euglena gracilis Z was examined with the electron microscope. The stigma was found to be a membrane-bounded organelle showing no close homology with the chloroplast or any other organelle. The structure and pigment content of the stigma both diminish with extended hetrotrophic growth, and quickly regain normal dimensions upon exposure to light. Synthesis of the red pigment is particularly sensitive to inhibition by chloramphenicol, whereas construction of the structure itself is specifically inhibited by cycloheximide.The paraflagellar body appears to consist of two sets of parallel 80 Å striations intersecting at 60°. It is within the flagellar membrane, but separated from the axoneme by another structure, the paraflagellar rod. This elongated structure has an ordered substructure which appears as intersecting sets of parallel striations; part of its basal portion projects as a circular flange which makes contact with the paraflagellar body.     

Yeast fatty acid synthase: structure to function relationship

The yeast fatty acid synthase is a multifunctional enzyme composed of two nonidentical subunits in an alpha 6 beta 6 complex that is active in synthesizing fatty acids. The seven catalytic activities required for fatty acid synthesis are divided between the alpha and beta subunits such that the alpha 6 beta 6 complex has six complements of each activity. It has been proposed that these are organized into six centers for fatty acid synthesis. There are different opinions regarding the operation of these centers in the alpha 6 beta 6 complex, on view being that they are functionally independent and the other proposes half-sites activity for the complex. We have attempted to distinguish between these proposals by the most direct method of active site titration, i.e., quantitation of fatty acyl product in the absence of turnover. This was accomplished by using p-nitrophenyl thioacetate and thiophenyl malonate (in place of the coenzyme A analogues) as substrates along with NADPH, thereby depriving the yeast synthase of coenzyme A required to release product as fatty acyl coenzyme A. The amount of fatty acyl product formed was quantitated by gas-liquid chromatography, as well as by direct estimation of radioactivity in the product when p-nitrophenyl thio [1-14C] acetate was used as a substrate. In both cases, a stoichiometry of close to six was found for mole of fatty acid synthesized per mole of alpha 6 beta 6 complex. This indicates that there are six functional centers for fatty acid synthesis in the multifunctional yeast alpha 6 beta 6 fatty acid synthase and that these centers operate independently.(ABSTRACT TRUNCATED AT 250 WORDS)     

Amylin and the amylin gene: structure, function and relationship to islet amyloid and to diabetes mellitus

Amylin, the major peptide component of the islet amyloid commonly found in the pancreases of patients with type 2 (non-insulin-dependent) diabetes mellitus (NIDDM), is a recently discovered islet polypeptide. This peptide has many structural and functional features suggesting that it is a novel hormone, which may control carbohydrate metabolism in partnership with insulin and other glucoregulatory factors. Amylin is synthesised in, and probably secreted from, the beta-cells of the islets of Langerhans, where it has recently been immunolocalised to secretory granules. DNA cloning studies indicate that in the human and the rat, amylin is generated from a precursor, preproamylin, which displays a typical signal peptide followed by a small prohormone-like sequence containing the amylin sequence. The presence of the signal peptide suggests that amylin is secreted and plays a physiological role. Amylin is probably generated by proteolytic processing similar to that for proinsulin and other islet prohormones. The human amylin gene encodes the complete polypeptide precursor in two exons which are separated by an intron of approx. 5 kb, and is located on chromosome 12. Amylin is a potent modulator of glycogen synthesis and glucose uptake in skeletal muscle, and is capable of inducing an insulin-resistant state in this tissue in vitro, and perhaps also in the liver in vivo. In normal metabolism, amylin could act in concert with insulin as a signal for the body to switch the site of carbohydrate disposal from glycogen to longer-term stores in adipose tissue, by making skeletal muscle relatively insulin-resistant, whilst at the same time leaving rates of insulin-stimulated carbohydrate metabolism in adipose tissue unaltered. Several lines of evidence now implicate elevated amylin levels in the pathogenic mechanisms underlying NIDDM, and suggest to us that the obesity which frequently accompanies this syndrome is a result of, rather than a risk factor for, NIDDM. Following the beta-cell destruction which occurs in type 1 (insulin-dependent) diabetes mellitus (IDDM), it is probable that amylin secretion disappears in addition to that of insulin. As patients with insulin-treated IDDM frequently experience problems with hypoglycaemia, and as amylin acts to modulate the action of insulin in various tissues, it is possible that amylin deficiency may contribute to morbidity in insulin-treated IDDM, perhaps through the loss of a natural damping mechanism which guards against hypoglycaemia under conditions of normal physiology.