微生物参与海草床元素循环及其生态修复功能

海草是分布在全球海岸带的沉水被子植物,与周围环境共同形成的海草床生态系统是三大典型海洋生态系统之一,具有十分重要的生态功能。20世纪以来,全球海草床衰退严重,研究海草床的生态修复迫在眉睫,现有修复方法未能足够重视微生物在海草床中的重要作用。本文综合阐述了微生物在海草床生态系统有机物矿化和营养流动过程中起到的作用,分析了微生物驱动下的海草床水体与沉积物之间的元素循环,提出了人类活动引起海草床退化的原因,总结了海草床微生物的系统研究方法,并在此基础上提出从微生物生态的角度修复海草床的新思路。     

Molecular approaches to problems in biogeochemical cycling

Summary By using molecular probe techniques in combination with activity and expression measurements, it is possible to estimate bacterial populations in nature. This information can be expooited to study a number of important environmental problems. For instance, it will be possible to study ecosystem perturbation and microbial competition, by altering an ecosystem or a laboratory model of an ecosystem, and assessing corresponding changes in key activities and populations. In addition, regulation of activities in the laboratory can be compared to the response of activities and populations in situ, to develop an understanding of the key parameters that control these processes in nature. These types of approaches are important steps for determining the role of microorganisms in geochemical cycling, in both specific habitats and on a global basis.     

Functions of the Epstein-Barr virus EBNA1 protein in viral reactivation and lytic infection

EBNA1 is the only nuclear Epstein-Barr virus (EBV) protein expressed in both latent and lytic modes of infection. While EBNA1 is known to play several important roles in latent infection, the reason for its continued expression in lytic infection is unknown. Here we identified two roles for EBNA1 in the reactivation of latent EBV to the lytic cycle in epithelial cells. First, EBNA1 depletion in latently infected cells was shown to positively contribute to spontaneous EBV reactivation, showing that EBNA1 has a role in suppressing reactivation. Second, when the lytic cycle was induced, EBNA1 depletion decreased lytic gene expression and DNA amplification, showing that it positively contributed to lytic infection. Since we have previously shown that EBNA1 disrupts promyelocytic leukemia (PML) nuclear bodies, we investigated whether this function could account for the effects of EBNA1 on lytic infection by repeating the experiments with cells lacking PML proteins. In the absence of PML, EBNA1 did not promote lytic infection, indicating that the EBNA1-mediated PML disruption is responsible for promoting lytic infection. In keeping with this conclusion, PML silencing was found to be sufficient to induce the EBV lytic cycle. Finally, by generating cells with single PML isoforms, we showed that individual PML isoforms were sufficient to suppress EBV lytic reactivation, although PML isoform IV (PML IV) was ineffective because it was most efficiently degraded by EBNA1. Our results provide the first function for EBNA1 in lytic infection and show that EBNA1 interactions with PML IV lead to a loss of PML nuclear bodies (NBs) that promotes lytic infection.     

Nitrogen deposition and its contribution to nitrogen cycling and associated soil processes

TIP1 is a gene defined by an X-ray induced allele tip1–2 and a previously described EMS-induced allele tip1−1 . TIP1 is involved in plant cell growth. tip1–2 plants display growth defects throughout the plant and exhibit defects in both root-hair and pollen-tube growth. tip1–2 plants are partly male sterile resulting from a combination of pollen germination and pollen-tube defects; their root-hairs are short, exhibit a tendency to branch and 2–4 hairs can initiate from each hair cell. They are also slightly dwarf in stature as a result of a general decrease in cell growth indicating that TIP1 activity is required for general cell growth. We propose a role for TIP in both the initiation and maintenance of growth in tip-growing cells. In addition TIP1 activity is required for normal cell expansion (non-tip cell growth) indicating that TIP1 is not exclusively involved in tip-growth.     

Global mRNA degradation during lytic gammaherpesvirus infection contributes to establishment of viral latency

During a lytic gammaherpesvirus infection, host gene expression is severely restricted by the global degradation and altered 3' end processing of mRNA. This host shutoff phenotype is orchestrated by the viral SOX protein, yet its functional significance to the viral lifecycle has not been elucidated, in part due to the multifunctional nature of SOX. Using an unbiased mutagenesis screen of the murine gammaherpesvirus 68 (MHV68) SOX homolog, we isolated a single amino acid point mutant that is selectively defective in host shutoff activity. Incorporation of this mutation into MHV68 yielded a virus with significantly reduced capacity for mRNA turnover. Unexpectedly, the MHV68 mutant showed little defect during the acute replication phase in the mouse lung. Instead, the virus exhibited attenuation at later stages of in vivo infections suggestive of defects in both trafficking and latency establishment. Specifically, mice intranasally infected with the host shutoff mutant accumulated to lower levels at 10 days post infection in the lymph nodes, failed to develop splenomegaly, and exhibited reduced viral DNA levels and a lower frequency of latently infected splenocytes. Decreased latency establishment was also observed upon infection via the intraperitoneal route. These results highlight for the first time the importance of global mRNA degradation during a gammaherpesvirus infection and link an exclusively lytic phenomenon with downstream latency establishment.     

Microbial diversity and biogeochemical cycling in soda lakes

Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art ‘meta-omic’ techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments.     

Modulation of Lactobacillus casei bacteriophage A2 lytic/lysogenic cycles by binding of Gp25 to the early lytic mRNA

The genetic switch of Lactobacillus casei bacteriophage A2 is regulated by the CI protein, which represses the early lytic promoter P_R and Cro that abolishes expression from the lysogenic promoter P_L. Lysogens contain equivalent cI and cro‐gp25 mRNA concentrations, i.e., CI only partially represses P_R, predicting a lytic cycle dominance. However, A2 generates stable lysogens. This may be due to Gp25 binding to the cro‐gp25 mRNA between the ribosomal binding site and the cro start codon, which abolishes its translation. Upon lytic cycle induction, CI is partially degraded, cro‐gp25 mRNA levels increase, and Cro accumulates, launching viral progeny production. The concomitant concentration increase of Gp25 restricts cro mRNA translation, which, together with the low but detectable levels of CI late during the lytic cycle, promotes reentry of part of the cell population into the lysogenic cycle, thus explaining the low proportion of L. casei lysogens that become lysed (～ 1%). A2 shares its genetic switch structure with many other Firmicutes phages. The data presented may constitute a model of how these phages make the decision for lysis versus lysogeny.     

A hierarchical approach to evaluating the significance of soil biodiversity to biogeochemical cycling

The significance of biodiversity to biogeochemical cycling is viewed most directly through the specific biogeochemical transformations that organisms perform. Although functional diversity in soils can be great, it is exceeded to a high degree by the richness of soil species. It is generally inferred from this richness that soil systems have a high level of functional redundancy. As such, indices of species richness probably contribute little to understanding the functioning of soil ecosystems. Another approach stresses the value of identifying keystone organisms, that is those that play an exceptionally important role in determining the structure and function of ecosystems. Both views tend to ignore the importance of biodiversity in maintaining the numerous and complex interactions among organisms in soils and their contributions to biogeochemical cycling. We describe some of those interactions and their importance to ecosystem function.Soil organisms alter the physical, chemical and biological properties of soils in innumerable ways. The composition and structure of biotic communities at one hierarchical level can influence the spatial heterogeneity of resource and refuge patches at other hierarchical levels. This spatial heterogeneity is supported by a number of biologically relevant spheres of influence that include the detritusphere, the drilosphere, the porosphere, the aggregatusphere and the rhizosphere. Each has fairly distinct properties that operate at different spatial scales. We discuss how these properties may function in regulating the interactions among organisms and the biogeochemical processes that they mediate. It is through the formation of a spatially and temporally heterogeneous structure that biodiversity may contribute most significantly to the functioning of soil ecosystems. Real advances in understanding the significance of biodiversity to biogeochemical cycling will come from taking a broader view of biodiversity. Such a view will necessarily encompass many levels of resolution including: 1) the importance of biodiversity to specific biogenic transformations, 2) the complexity and specificity of biotic interactions in soils that regulate biogeochemical cycling, and 3) how biodiversity may operate at different hierarchically arranged spatial and temporal scales to influence the structure and function of ecosystems.     

The contribution of genetic variation and infection to the pathogenesis of ANCA-associated systemic vasculitis

The aetiology of anti-neutrophil cytoplasmic antibody (ANCA)-associated systemic vasculitis has not been well defined. Here we review two factors which may play a role in the pathogenesis of the disease: genetics and infection. In particular, we discuss the role of autoantibodies to LAMP-2, which may arise following infection with Gram-negative bacteria, and may contribute to the development of ANCA-associated systemic vasculitis in genetically susceptible individuals.     

Enzymes and biogeochemical cycling in wetlands during a simulated drought

Possible interactions between soil enzymes and thebiogeochemistry of wetlands were investigated duringa field-based drought simulation. Under control(waterlogged) conditions, correlations were foundbetween the activity of the enzyme B-glucosidase andtwo properties associated with carbon cycling, namelyi) CH₄ release r = 0.79,p lt 0.01) and ii) dissolvedorganic carbon concentration (r= -0.81, p lt 0.01). In contrast,the transition to drought conditions resulted in correlations betweenB-glucosidase activity and certain mineralisationprocesses, namely the release of mg and Ca(r = 0.72, p lt 0.05). Sulphataseactivity correlated with changes in sulphate concentration during the droughtsimulation (r = 0.73, p lt 0.05).Further support for the suggested enzymic involvement in biogeochemicalprocesses was found in laboratory studies. Theseexperiments indicated that increasing the abundance ofB-glucosidase could stimulate trace gas emissions(p lt 0.001) and increase the concentration ofmagnesium and calcium (p lt 0.05). Increasedsulphatase abundance caused a suppression of methane emissions(p = 0.053).     

The role of particles on the biogeochemical cycling of domoic acid and its isomers in natural water matrices

The adsorption of dissolved domoic acid (DA) and its geometrical isomers was assessed in aqueous solutions containing various types of particles. In one series of experiments carried out in coastal seawater, detectable net adsorption of 100 nM DA occurred only onto natural seawater particles (unfiltered seawater) and 0.5 g L⁻¹ chromatographic silica (18%) in 0.2 μm-filtered seawater. Some net adsorption (<5%) also occurred in the 0.5 g L⁻¹ suspension of estuarine sediment and 0.5 g L⁻¹ solution of humic acid in filtered seawater. No losses were seen in 0.5 g L⁻¹ suspensions of illite, kaolinite, montmorillonite, and silica sand. Biological degradation accounted for small losses (8–10%) in filtered seawater without particles. A second series of experiments using organic-free, <5 μm fractions of kaolinite and montmorillonite in deionized water (DIW) demonstrated that 70% of DA adsorbed onto kaolinite, but only 5% onto montmorillonite. Geometrical isomers of DA (iso-DA D, E, and F) showed negligible adsorption (0–8%) onto a variety of particles in filtered seawater, suggesting that major ions in seawater neutralize electrostatic attractions between particles and DA isomers. These results suggest that DA and its isomers are relatively hydrophilic and not particle reactive. Our data suggest that photochemical and biological degradation of dissolved DA and its isomers appears to occur in bulk surface seawater and its transport to bottom sediments must be mainly biologically driven.     

An introduction to the biogeochemical cycling of calcium and substitutive strontium in living coral reef mesocosms

The coral reef mesocosms designed by the Smithsonian Institution's Dr. Walter Adey, his Marine System Laboratory personnel, and staff members of the Pittsburgh Aqua-Zoo simulate most of the physical, chemical, and biological parameters found in natural Caribbean coral reefs. After developing the mesocosm in Pittsburgh, an evaluation and comparison between natural reef seawater sources and closed mesocosm seawater conditions indicated that an additional parameter should be investigated. It was hypothesized that, given time, the aragonite- and calcite (CaCO₃ crystal forms)-producing organisms in the closed mesocosms could deplete the seawater of available Ca²⁺ and substitutive Sr²⁺. Atomic absorption spectrophotometry was utilized to determine concentrations in the seawater over time. Results showed a substantial reduction in dissolved Ca and Sr in the mesocosm after approximately two years. Dissolved aragonitic Halimeda algae parts were put into the system for replacive purposes. In terms of the biogeochemical cycling of Ca²⁺ and Sr²⁺, the coral reef mesocosm organisms behaved similarly to natural reefs, which have a constant supply of dissolved Ca²⁺ and Sr²⁺. Further research utilizing radiolabeled sources of Ca²⁺, Sr²⁺, and Mg²⁺, in conjunction with in vivo scanning electron microscopy (SEM) and growth increment studies, are recommended for determining the exact biogeochemical pathways for these elements in coral reefs, and to quantify growth parameters. © 1993 Wiley-Liss, Inc.     

Some thoughts on the biogeochemical cycling of potassium in terrestrial ecosystems

Biogeochemistry - Potassium presents a conundrum for biogeochemists. Potassium is cycled wastefully at the plant level, but it appears to be conserved in the nutrient budgets of entire ecosystems,...     

NK and NKT cell-independent contribution of interleukin-15 to innate protection against mucosal viral infection

Interleukin-15 (IL-15) is essential for the development, maturation, and function of NK and NKT cells, which are critical components of the innate immune defense against viral infections. We recently showed that mice lacking IL-15 and/or NK/NKT cells are significantly more susceptible to intravaginal (IVAG) herpes simplex virus type 2 (HSV-2) infection than control mice. For this study, we examined whether IL-15 has any direct antiviral activity, independent of NK/NKT cells, in innate protection against HSV-2 infection. A sensitive enzyme-linked immunosorbent assay for murine IL-15 was developed and used to show that IVAG HSV-2 infection induces IL-15 in vaginal washes. Using immunohistochemistry, we detected IL-15-positive cells in the submucosa and vaginal epithelium following IVAG HSV-2 infection. Local, but not systemic, delivery of murine recombinant IL-15 (mrIL-15) to the genital mucosae of IL-15(-/-) and RAG-2(-/-) gamma(c)(-/-) mice, which both lack NK and NKT cells, resulted in significant reductions in HSV-2 titers in genital washes and 60% survival following IVAG HSV-2 challenge. Furthermore, we showed that IL-15 is important for CpG oligodeoxynucleotide (ODN)-induced innate protection against genital HSV-2 infection. While 100% of CpG ODN-treated RAG2(-/-) gamma(c)(-/-) mice, which are capable of producing IL-15 but lack NK/NKT cells, survived an IVAG HSV-2 challenge, only 60% of CpG ODN-treated IL-15(-/-) mice survived, and all of these mice had similar vaginal viral titers to those in control mice by day 3 postchallenge. Lastly, a treatment of RAW264.7 cells with mrIL-15 induced the production of tumor necrosis factor alpha and beta interferon (IFN-beta), but not IFN-alpha, and significantly protected them against HSV-2 infection in vitro. The results of these studies indicate that IL-15 can act independently of NK/NKT cells in mediating the innate defense against viral infection.     

Isolation and preliminary characterization of lytic and lysogenic phages with wide host range within the streptomycetes

Examination of approximately 700 soil samples yielded about 100 actinophages. Restriction analysis of phage DNA indicated that 57 are unique, and of these, 20 produce turbid plaques on one or more of the streptomycetes tested. Five phages are shown to insert into the genome of Streptomyces avermitilis. None of the phages was able to perform generalized transduction of S. avermitilis.     

Dopamine transmission in the tail striatum: Regional variation and contribution of dopamine clearance mechanisms

The striatum can be divided into four anatomically and functionally distinct domains: the dorsolateral, dorsomedial, ventral and the more recently identified caudolateral (tail) striatum. Dopamine transmission in these striatal domains underlies many important behaviours, yet little is known about this phenomenon in the tail striatum. Furthermore, the tail is divided anatomically into four divisions (dorsal, medial, intermediate and lateral) based on the profile of D₁ and D₂ dopamine receptor-expressing medium spiny neurons, something that is not seen elsewhere in the striatum. Considering this organisation, how dopamine transmission occurs in the tail striatum is of great interest. We recorded evoked dopamine release in the four tail divisions, with comparison to the dorsolateral striatum, using fast-scan cyclic voltammetry in rat brain slices. Contributions of clearance mechanisms were investigated using dopamine transporter knockout (DAT-KO) rats, pharmacological transporter inhibitors and dextran. Evoked dopamine release in all tail divisions was smaller in amplitude than in the dorsolateral striatum and, importantly, regional variation was observed: dorsolateral ≈ lateral > medial > dorsal ≈ intermediate. Release amplitudes in the lateral division were 300% of that in the intermediate division, which also exhibited uniquely slow peak dopamine clearance velocity. Dopamine clearance in the intermediate division was most dependent on DAT, and no alternative dopamine transporters investigated (organic cation transporter-3, norepinephrine transporter and serotonin transporter) contributed significantly to dopamine clearance in any tail division. Our findings confirm that the tail striatum is not only a distinct dopamine domain but also that each tail division has unique dopamine transmission characteristics. This supports that the divisions are not only anatomically but also functionally distinct. How this segregation relates to the overall function of the tail striatum, particularly the processing of multisensory information, is yet to be determined.

     

Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution

Populations of RNA viruses are often characterized by abundant genetic variation. However, the relative fitness of these mutations is largely unknown, although this information is central to our understanding of viral emergence, immune evasion, and drug resistance. Here we develop a phylogenetic method, based on the distribution of nonsynonymous and synonymous changes, to assess the relative fitness of polymorphisms in the structural genes of 143 RNA viruses. This reveals that a substantial proportion of the amino acid variation observed in natural populations of RNA viruses comprises transient deleterious mutations that are later purged by purifying selection, potentially limiting virus adaptability. We also demonstrate, for the first time, the existence of a relationship between amino acid variability and the phylogenetic distribution of polymorphisms. From this relationship, we propose an empirical threshold for the maximum viable deleterious mutation load in RNA viruses.     

A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes

RNA viruses successfully adapt to various environments by repeatedly producing new mutants, often through generating a number of nucleotide substitutions. To estimate the degree of variation in mutation rates of RNA viruses and to understand the source of such variation, we studied the synonymous substitution rate because synonymous substitution is exempt from functional constraints at the protein level, and its rate reflects the mutation rate to a great extent. We estimated the synonymous substitution rates for a total of 49 different species of RNA viruses, and we found that the rates had tremendous variation by 5 orders of magnitude (from 1.3 x 10(-7) to 6.2 x 10(-2) /synonymous site/year). Comparing the synonymous substitution rates with the replication frequencies and replication error rates for the RNA viruses, we found that the main source of the rate variation was differences in the replication frequency because the rates of replication error were roughly constant over different RNA viruses. Moreover, we examined a relationship between viral life strategies and synonymous substitution rates to understand which viral life strategies affect replication frequencies. The results show that the variation of synonymous substitution rates has been influenced most by either the difference in the infection modes or the differences in the transmission modes. In conclusion, the variation of mutation rates for RNA viruses is caused by different replication frequencies, which are affected strongly by the infection and transmission modes.