A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales

This study uses a set of PCR-based methods to examine the putative microbiota associated with lichen thalli. In initial experiments, generalized oligonucleotide-primers for the 16S rRNA gene resulted in amplicon pools populated almost exclusively with fragments derived from lichen photobionts (i.e., Cyanobacteria or chloroplasts of algae). This effectively masked the presence of other lichen-associated prokaryotes. In order to facilitate the study of the lichen microbiota, 16S ribosomal oligonucleotide-primers were developed to target Bacteria, but exclude sequences derived from chloroplasts and Cyanobacteria. A preliminary microbiotic survey of lichen thalli using these new primers has revealed the identity of several bacterial associates, including representatives of the extremophilic Acidobacteria, bacteria in the families Acetobacteraceae and Brucellaceae, strains belonging to the genus Methylobacterium, and members of an undescribed lineage in the Rhizobiales. This new lineage was investigated and characterized through molecular cloning, and was found to be present in all examined lichens that are associated with green algae. There is evidence to suggest that members of this lineage may both account for a large proportion of the lichen-associated bacterial community and assist in providing the lichen thallus with crucial nutrients such as fixed nitrogen.     

Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

Symbioses represent a frequent and successful lifestyle on earth and lichens are one of their classic examples. Recently, bacterial communities were identified as stable, specific and structurally integrated partners of the lichen symbiosis, but their role has remained largely elusive in comparison to the well-known functions of the fungal and algal partners. We have explored the metabolic potentials of the microbiome using the lung lichen Lobaria pulmonaria as the model. Metagenomic and proteomic data were comparatively assessed and visualized by Voronoi treemaps. The study was complemented with molecular, microscopic and physiological assays. We have found that more than 800 bacterial species have the ability to contribute multiple aspects to the symbiotic system, including essential functions such as (i) nutrient supply, especially nitrogen, phosphorous and sulfur, (ii) resistance against biotic stress factors (that is, pathogen defense), (iii) resistance against abiotic factors, (iv) support of photosynthesis by provision of vitamin B₁₂, (v) fungal and algal growth support by provision of hormones, (vi) detoxification of metabolites, and (vii) degradation of older parts of the lichen thallus. Our findings showed the potential of lichen-associated bacteria to interact with the fungal as well as algal partner to support health, growth and fitness of their hosts. We developed a model of the symbiosis depicting the functional multi-player network of the participants, and argue that the strategy of functional diversification in lichens supports the longevity and persistence of lichens under extreme and changing ecological conditions.     

岸滩粪便污染指示菌来源与影响因素研究进展

粪便污染指示菌(Fecal Indicator Bacteria,FIB),如大肠杆菌、肠球菌和耐热大肠菌等是用于指示水体中污染程度的微生物,但近年来的研究表明岸滩逐步成为FIB的重要储存库.微生物源示踪技术(Microbial Source Tracking,MST)等方法被广泛应用于溯源岸滩FIB污染,但FIB进入...     

Free radical scavenging and antioxidant potential of mangrove plants: a review

Free radicals derived from reactive oxygen species and reactive nitrogen species are generated in our body by normal cellular metabolism which is enhanced under stress conditions. The most vulnerable biological targets of free radicals are cell structures including proteins, lipids and nucleic acids. Since antioxidants synthesized in the body are not sufficient under oxidative stress, their exogenous supply is important to prevent the body from free radical-induced injury. Recent researches have shown that antioxidants of plant origin with free radical scavenging property could have great importance as therapeutic agents in management of oxidative stress. Mangrove plants growing in inhospitable environment of the intertidal regions of land and sea in tropics and sub-tropics are equipped with very efficient free radical scavenging system to withstand the variety of stress conditions. These mangrove plants possess variety of phytochemical and are rich in phenolic compounds such as flavonoids, isoflavones, flavones, anthocyanins, coumarins, lignans, catechins, isocatechins, etc., which served as source of antioxidants. Isolation and identification of these antioxidant compounds offer great potential for their pharmaceutical exploitations. However, no comprehensive literature is available on antioxidants’ studies in mangrove plants in particular. Hence, the present review discusses the antioxidant potential of mangrove plants with its specific role under salt stress as well as the progress made so far in evaluation of antioxidant activities of different mangrove species.     

小麦赤霉病拮抗菌JB7的拮抗活性及鉴定

由禾谷镰刀菌(Fusarium graminearum, Fg)引起的赤霉病是限制小麦生产的主要病害之一。生物防治是一种高效且可持续的防治方法。【目的】从小麦种子内筛选具有抑制禾谷镰刀菌的菌株并对其生防潜力进行评估,为小麦赤霉病生防制剂的开发与利用提供菌种资源及理论支撑。【方法】采用平板对峙、孢子萌发法和无菌上清液抑菌试验筛选小麦种子内对禾谷镰刀菌具有拮抗活性的内生菌株;利用扫描电镜(scanning electron microscope, SEM)和共聚焦扫描电镜(confocal laser scanning microscope, CLSM)观察并分析无菌上清液对Fg的分生孢子形态、膜完整性以及胞内活性氧的影响;通过盆栽试验验证内生菌对小麦赤霉病的生防效果;应用二代Illumina HiSeq测序平台进行全基因组测序。【结果】从小麦种子中分离出一株高效抑制Fg生长的内生菌株JB7,其衰亡期无菌上清液对Fg孢子萌发抑制率高达85.23%。菌株JB7的无菌上清液使Fg孢子表面凹陷,破坏其细胞膜,造成核酸和蛋白质的渗漏,诱导Fg菌丝活性氧的累积,引起Fg菌丝可溶性蛋白和丙二醛含量的显著升高。该菌株具有分泌蛋白酶、纤维素酶、葡聚糖酶和产铁载体的能力。盆栽试验表明菌株JB7能显著降低小麦赤霉病的病情指数(P<0.05)。经全基因组学鉴定为甲基营养型芽孢杆菌(Bacillus methylotrophicus) JB7,该菌株基因组中含有12个抑菌功能的次级代谢产物合成基因簇。【结论】菌株JB7能抑制禾谷镰刀菌的生长,对小麦赤霉病有较强的防效,可作为生物防治小麦赤霉病的候选菌株。     

烟草根际铁载体产生菌G-229-21T的筛选、鉴定及拮抗机理

[目的]从烟草根际筛选烟草疫霉[Phytophthora parasitica var.nicotianae(Breda de Hann)Tucker]拮抗菌,探索其拮抗机理.[方法]限铁(2.0 μmol/L FeCl3)蔗糖-天冬酰胺平板对峙法筛选烟草疫霉拮抗菌;刃天青(CAS)法检测其铁载体的产生及其对铁离子的亲和能力.结合形态、生理生化、16s rRNA序列同源性和系统发育分析及种特异性分子法对其进行鉴定.XAD-2吸附层析法提取其铁载体,分光光度法检测其铁载体类型.不同铁离子浓度下,比较其铁载体对烟草疫霉的抑制作用.[结果]我们筛选到一株限铁条件下烟草疫霉拮抗菌G-229-21T,该菌产生高亲和力铁载体,被初步鉴定为Pseudomonas mediterranea.该菌产生的羧酸型铁载体,在低铁条件下(0.16μmol/L～10μmol/L,FeCl3)对烟草疫霉的抑制率达92.3%以上,而在富铁条件下(100 μmol/L FeCl3)抑制率仅为2.0%.[结论]首次报道P. mediterranea G-229-21T产生高亲和力羧酸型铁载体,该铁载体在低铁条件下对烟草疫霉有显著的抑制作用.     

Viability and activity in readily culturable bacteria: a review and discussion of the practical issues

In microbiology the terms viability and culturability are often equated. However, in recent years the apparently self-contradictory expression viable-but-nonculturable (VBNC) has been applied to cells with various and often poorly defined physiological attributes but which, nonetheless, could not be cultured by methods normally appropriate to the organism concerned. These attributes include apparent cell integrity, the possession of some form of measurable cellular activity and the apparent capacity to regain culturability. We review the evidence relating to putative VBNC cells and stress our view that most of the reports claiming a return to culturability have failed to exclude the regrowth of a limited number of cells which had never lost culturability. We argue that failure to differentiate clearly between use of the terms viability and culturability in an operational versus a conceptual sense is fuelling the current debate, and conclude with a number of proposals that are designed to help clarify the major issues involved. In particular, we suggest an alternative operational terminology that replaces VBNC with expressions that are internally consistent.     

Nutrient requirement for UASB process: a review

In literature, numerous studies regarding nutrients dosing are available in UASB reactors. Various nutrients and tracemetals used in UASB studies include nitrogen, phosphorous, yeast extract, magnesium, potassium, calcium, sulphur, iron, aluminium, zinc, nickel, cobalt, molybdenum, manganese, copper, boron, selenium, citrate, resazurine, EDTA, and hydrochloric acid. Often, there is a wide variation in the composition and quantification of nutrients and tracemetals, used to supplement the influent feed in UASB reactors. In this paper, nutrients and tracemetals formulations used in different studies on UASB reactors are compiled and critically analysed. In order to have uniformity, concentrations of nutrients and tracemetals have been converted into equivalent terms as g nutrients or tracemetals/g of waste COD. The ranges for this ratio for all the constituents of nutrients and tracemetals are given. Besides, the ranges associated with minimum start-up periods are also obtained. It is hoped that the information presented in this study would facilitate the nutrients dosing in UASB reactors.     

Antimutagenic properties of bacteria: a review

Lactic acid and propionic acid bacteria, bifidobacteria, and fecal enterococci associated with the activity of humans and animals caused antimutagenic effects (AME) on many test systems designed for detecting point mutations and chromosomal aberrations. Bacterial cells and some of their metabolites attenuate the mutagenic action of several genotoxic agents, and this effect is mediated by the mechanism of dysmutagenesis and/or bioantimutagenesis. Possible mechanisms of various AMEs and possible practical applications of antimutagenic properties of bacteria are discussed.     

Early hominid hunting and scavenging: A zooarcheological review

Before the early 1980s, the prevailing orthodoxy in paleoanthropology considered Early Stone Age archeological sites in East Africa to represent a primitive form of hominid campsites. The faunal evidence preserved in these sites was viewed as the refuse of carcass meals provided by hominid males in a social system presumptively characterized by sexual division of labor. This interpretation of early hominid life ways, commonly known as the “Home Base” or “Food Sharing” model, was developed most fully by Glynn Isaac.^1–4 As Bunn and Stanford⁵ emphasized, this model was greatly influenced by a paradigm that coalesced between 1966 and 1968, referred to as “Man the Hunter.”⁶     

Plant carbohydrate scavenging through tonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria

TonB-dependent receptors (TBDRs) are outer membrane proteins mainly known for the active transport of iron siderophore complexes in Gram-negative bacteria. Analysis of the genome of the phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc), predicts 72 TBDRs. Such an overrepresentation is common in Xanthomonas species but is limited to only a small number of bacteria. Here, we show that one Xcc TBDR transports sucrose with a very high affinity, suggesting that it might be a sucrose scavenger. This TBDR acts with an inner membrane transporter, an amylosucrase and a regulator to utilize sucrose, thus defining a new type of carbohydrate utilization locus, named CUT locus, involving a TBDR for the transport of substrate across the outer membrane. This sucrose CUT locus is required for full pathogenicity on Arabidopsis, showing its importance for the adaptation to host plants. A systematic analysis of Xcc TBDR genes and a genome context survey suggested that several Xcc TBDRs belong to other CUT loci involved in the utilization of various plant carbohydrates. Interestingly, several Xcc TBDRs and CUT loci are conserved in aquatic bacteria such as Caulobacter crescentus, Colwellia psychrerythraea, Saccharophagus degradans, Shewanella spp., Sphingomonas spp. or Pseudoalteromonas spp., which share the ability to degrade a wide variety of complex carbohydrates and display TBDR overrepresentation. We therefore propose that TBDR overrepresentation and the presence of CUT loci designate the ability to scavenge carbohydrates. Thus CUT loci, which seem to participate to the adaptation of phytopathogenic bacteria to their host plants, might also play a very important role in the biogeochemical cycling of plant-derived nutrients in marine environments. Moreover, the TBDRs and CUT loci identified in this study are clearly different from those characterized in the human gut symbiont Bacteroides thetaiotaomicron, which allow glycan foraging, suggesting a convergent evolution of TBDRs in Proteobacteria and Bacteroidetes.     

Cultivable bacteria isolated from apple trees cultivated under different crop systems: Diversity and antagonistic activity against Colletotrichum gloeosporioides

This study evaluated the diversity of cultivable plant growth-promoting (PGP) bacteria associated with apple trees cultivated under different crop management systems and their antagonistic ability against Colletotrichum gloeosporioides. Samples of roots and rhizospheric soil from apple trees cultivated in organic and conventional orchards in southern Brazil were collected, together with soil samples from an area never used for agriculture (native field). Bacteria were identified at the genus level by PCR-RFLP and partial sequencing of the 16S rRNA, and were evaluated for some PGP abilities. The most abundant bacterial genera identified were Enterobacter (27.7%), Pseudomonas (18.7%), Burkholderia (13.7%), and Rahnella (12.3%). Sixty-nine isolates presented some antagonist activity against C. gloeosporioides. In a greenhouse experiment, five days after exposure to C. gloeosporioides, an average of 30% of the leaf area of plants inoculated with isolate 89 (identified as Burkholderia sp.) were infected, whereas 60 to 73% of the leaf area of untreated plants was affected by fungal attack. Our results allowed us to infer how anthropogenic activity is affecting the bacterial communities in soil associated with apple tree crop systems, and to obtain an isolate that was able to delay the emergence of an important disease for this culture.     

稻株上拮抗细菌的定殖及其对土著细菌的影响

在温室条件下,通过分批播种、接种纹枯病菌Rhizoctonia solani,以及在水稻分孽盛期喷雾拮抗细菌Pseudomonas fluorescens Pf7-14 (天然的抗萘啶酮酸菌株) 和B5423-R(Bacillus subtilis B5423的利福平抗性突变体)的菌悬浮液,并通过定期取样,平板系列稀释法回收,测定了菌株Pf7-14、B5423-R和土著细菌群体在水稻健株和纹枯病株上的种群数量,所获结果如下:①当相同的浓度(约2.0×108cfu/ml)的菌悬浮液喷雾到叶片时,菌株Pf7-14定殖的时间比菌株B5423-R长,且在相同的时间内,菌株Pf7-14的平均群体数量高于菌株B5423-R;②在健康的水稻茎部,菌株Pf7-14的两个高、低不同浓度处理的平均群体数量均表现出随时间降低的趋势;相比,较低浓度(4.0×107cfu/ml)的B5423-R在茎部的平均群体数量随着时间的下降,而较高浓度(2.0×108cfu/ml)的B5423-R的平均群体数量在水稻乳熟至黄熟期保持稳定或略有增长;③当病斑面积占取样茎面积的比率为20%～35%时,在应用1和14d后菌株Pf7-14在健茎的平均群体数量分别是病茎的6倍多和2倍多,差异均达到显著性的水平(P=0.05),而菌株B5423-R 在应用1d后病茎的数量比在健茎显著性地低大约1倍,但在7～14d后,病茎的数量比在健茎显著性地高5～6倍,群体在病茎表现出相对的增长;④土著细菌群体在病斑茎部是健茎的6～7倍.这些结果表明两类拮抗细菌有着明显不同的定殖习性,在病斑上B5423比Pf7-14具有更强的竞争能力,是一类更好的生防制剂;同时表明引入的拮抗细菌同土著细菌群体在营养和空间上竞争激烈,且土著细菌群体更具有竞争优势.     

棉花黄萎病拮抗细菌产铁载体测定及其对抑菌活性的影响

【背景】棉花是新疆农业的支柱产业,棉花黄萎病严重影响棉花产量和纤维品质,有效的防治途径是目前解决的首要任务。【目的】探究BacillusvelezensisBHZ-29、Bacillusatrophaeus SHZ-24、Bacillus subtilis SHT-15、Bacillus vanillea SMT-24菌株产铁载体能力及其对抑菌活性的影响。【方法】MKB-CAS双层平板检测铁载体,Arnow法与高氯酸铁法鉴定铁载体类型,CAS染液定量铁载体,琼脂扩散法测定低铁条件下铁载体对抑菌物质的影响。【结果】MKB-CAS固体平板菌体周围出现橙紫色显色反应,Arnow实验4株拮抗菌反应液颜色为红色,高氯酸铁实验反应液颜色为黄色;BHZ-29、SHZ-24、SHT-15、SMT-24菌株铁载体定量活性单位最大值分别为8.27%±0.61%、31.80%±2.06%、16.06%±3.61%、15.53%±0.51%,吸光度值As/Ar比值最小分别为0.917±0.092、0.682±0.021、0.845±0.005、0.846±0.008。BHZ-29、SHZ-24、SMT-24菌株含铁离子浓度0、10、20μmol/L 3组处理发酵无菌滤液均未出现抑菌圈,SHT-15菌株3组处理出现抑菌圈,抑菌圈直径大小无差异性。【结论】4株拮抗菌株均产铁载体,铁载体类型为儿茶酚型,4株拮抗菌株整体产铁载体能力较低,最高达31.80%±2.06%,产铁能力As/Ar比值高于0.682时,BHZ-29、SHZ-24、SMT-24菌株含铁离子浓度0、10、20μmol/L 3组处理发酵无菌滤液对抑菌活性无影响,SHT-15菌株3组不同铁离子浓度处理对抑菌物质影响差异不显著。     

白色念珠菌拮抗菌株的筛选

目的筛选对白色念珠菌具有明显拮抗作用的菌株.方法通过纸片琼脂扩散法(K-B法)观察各菌株对白色念珠菌的拮抗作用;再利用试管法观察有拮抗作用菌株对白色念珠菌的抑菌效果.结果 K-B法表明大肠埃希菌、甲型链球菌和卡他球菌对白色念珠菌无抑菌作用,表皮葡萄球菌、微球菌有抑菌作用,但抑菌环小;枯草杆菌有明显抑菌作用.试管法表明表皮葡萄球菌和枯草杆菌对白色念珠菌均有生物拮抗作用,其抑菌率分别为97%和89.7%.结论枯草杆菌是白色念珠菌的理想拮抗菌株.     

Influence of soil factors and cultural practice on biological control of sheath blight of rice with antagonistic bacteria

Fluorescent and nonfluorescent strains of bacteria isolated from rice rhizospheres on the International Rice Research Institute (IRRI) farm were evaluated for in vitro antibiosis towards the sheath blight (ShB) pathogen Rhizoctonia solani, and for suppression of ShB in detached rice leaves. Efficient strains were located on the basis of consistent performance in two laboratory tests. Among nine efficient strains, 3 strains were identified as Pseudomonas fluorescens, 5 strains were tentatively identified as Bacillus spp. and one strain was identified as Enterobacter. In three greenhouse tests lowland rice soils with optimum pH for rice growth (pH 5.5–6.5), acidic pH (pH 5.0) and boron toxicity were found more suitable for biological control of ShB and, less frequently, also yield increases than were alkaline (pH 6.9) and zinc-deficient soils. Bacterial treatments afforded significant ShB reductions in 3 field experiments, but no significant yield increases resulted. In direct-seeded rice best performances by bacterial treatments in terms of ShB suppression were 66 and 98% during DS 1988 and WS 1988, respectively, which were comparable to or better than the performance of validamycin (a fungicide routinely used for ShB control) which afforded 42 and 63% disease suppression, respectively, in the same experiments. Although bacterial treatments caused ShB reductions both in direct-seeded and transplanted rice crops, disease control was more pronounced in direct-seeded than in transplanted crops. These results indicate that carefully selected strains of bacterial antagonists have the potential for ShB suppression in rice at least in areas where direct-seeding is practised.     

硫酸盐还原细菌生物被膜的形成与调控研究进展

硫酸盐还原细菌(sulfate-reducing bacteria,SRB)形成的生物被膜是微生物导致金属锈蚀行为的主要原因,同时也是重金属污水微生物修复技术的关键因子。生物被膜形成及调控机制研究对SRB的防治和利用均十分重要。本文综述了近年来SRB生物被膜的研究进展,包括SRB生物被膜的胞外多聚物组成和控制因子,并着重阐述了目前已知的调控因子对SRB生物被膜形成的影响。     

Enhancement of algicidal activity by immobilization of algicidal bacteria antagonistic to Stephanodiscus hantzschii (Bacillariophyceae)

AIMS: Enhancement of algicidal activity by immobilization of algicidal bacteria antagonistic to Stephanodiscus hantzschii. METHODS AND RESULTS: In laboratory studies, A diatom-lysing bacterium, Pseudomonas fluorescens HYK0210-SK09 showed strong algicidal activity against S. hantzschii, but a natural mesocosm study revealed that this bacterium failed to fully control natural blooms of Stephanodiscus at the low water temperatures that favour these blooms. Here, we sought to develop an effective immobilization strategy for enhancing the algicidal activity of HYK0210-SK09 in the natural setting. Bacterium HYK0210-SK09 was immobilized with various carriers including agar, alginate, polyurethane and cellulose sponge. The bacterial cells immobilized with cellulose sponge (CIS) induced more rapid and complete lysis of S. hantzschii than other carriers, and had a higher packing ability than polyurethane. Furthermore, CIS-immobilized cells showed higher lysis of S. hantzschii at the same concentrations as that of free cells (< or =1 x 10(7) cells ml(-1)), and had especially strong algicidal activity at the low temperatures (<10 degrees C). Based on these laboratory studies, we assessed the possible application of HYK0210-SK09 cells in the field by performing a mesocosm study during the winter season. The CIS-immobilized cells with species-specific activity towards the genera Stephanodiscus showed extremely high algicidal activity (up to 95%) against a bloom of Stephanodiscus hantzschii even at low water temperatures, because of high cell packing and subsequent cell protection against low temperatures and predators, whereas free cells showed negligible algicidal activities under these conditions. CONCLUSION: Immobilizing cells of HYK0210-SK09 in CIS foam, rather than in the other matrices tested, could achieve more efficient control of Stephanodiscus blooms and showed a significant algicidal activity on in vitro and in vivo blooms, even at low water temperature. SIGNIFICANCE AND IMPACT OF THE STUDY: Collectively, these results indicate that CIS of algicidal bacteria may form an important strategy for effective management of Stephanodiscus blooms at low water temperatures.     

Environmental factors associated with proteolytic activity of estuarine bacteria

The effects of various parameters on the extracellular hydrolysis of protein by salt marsh bacteria were examined using an agar plate assay technique. Maximum activity was observed at pH 8 and 18 C. Elimination of salts and nutrients from the growth media had little effect on activity; while, incubation in a reduced oxygen atmosphere markedly restricted proteolysis by laboratory stocks and random isolates. The availability of oxygen appeared to be one of the important factors controlling extracellular protease production by salt marsh bacteria.     

相似穿孔线虫拮抗细菌的筛选及分子鉴定

【背景】相似穿孔线虫是一种重要的检疫性有害生物,其寄主范围广,危害具有毁灭性,已给我国农业生产造成潜在威胁。由于目前大多化学杀线剂毒性较高,筛选获得对相似穿孔线虫具有拮抗活性的微生物菌株对线虫防控具有重要意义。【方法】广泛从染病香蕉植株根际采集土壤样本,运用等比稀释涂布平板法分离菌株;采用摇瓶发酵法制备拮抗菌株上清液和发酵液。通过室内生物测定和盆栽试验,筛选出对相似穿孔线虫具有拮抗作用的细菌菌株,并通过16S rDNA的PCR扩增和序列分析,对拮抗菌株进行种类鉴定。【结果】获得5株对相似穿孔线虫具有较理想拮抗活性的细菌菌株。其中,菌株HD-86的作用效果最好,其发酵上清液处理24 h后的相似穿孔线虫死亡率达100%。盆栽试验表明,菌株HD-86发酵液处理42和70 d后对相似穿孔线虫的相对防效分别为77.34%和90.51%,均优于对照药剂阿维菌素。【结论与意义】菌株HD-86对相似穿孔线虫具有很强的拮抗作用,将其鉴定为洋葱伯克氏菌Burkholderia cepacia。本研究可为相似穿孔线虫生防制剂的研发和病害的防控提供依据。