豆科植物根瘤中非共生的内生菌遗传多样性研究进展

在豆科植物与根瘤菌之间结合形成的固氮共生体中,其典型的特征是由特定的微共生体诱导形成的根瘤或茎瘤,除了根瘤菌外,在根瘤中同样也分离出多种与根瘤菌共生固氮无关的内生菌类群,而且根瘤菌与内生菌通常可以共存于同一个根瘤内是普遍存在的客观现象,这些非共生的内生菌生活史的一部分存在于根瘤内且不会引起植物发病,但有关它们的生态学作用还知之甚少,由于其生态上的重要性,近年来对该现象的研究不断深入.就近年来根瘤中隶属于变形菌门,放线菌门、后壁菌门的非共生的内生菌遗传多样性所取得的最新研究结果进行了总结,并介绍了根瘤中相关内生菌多样性研究的新进展.同时,指出了该研究领域存在的问题,并对未来相关研究方向做了展望.     

Morphogenesis of lucerne root nodules incited by Rhizobium meliloti in the presence of combined nitrogen

Combined light and transmission electron microscopy were used to examine the effect of nitrate on the development of root nodules in lucerne (alfalfa, Medicago sativa L.) following induction by the nitrogen-fixing symbiont, Rhizobium meliloti. The timing of NO ₃ ^- addition was varied in order to study its effect on all of the recognized morphogenetic steps of nodule formation. Roots of plants inoculated in the presence of 18 mM NO ₃ ^- had straight root hairs which were devoid of adherent rhizobia and infection threads, and developed no nodules. However, nodules were formed on roots if 18 mM NO ₃ ^- was added 5 d after inoculation. At this time, the initiation of nodule primordia had already commenced in the root cortex. The histology and ultrastructure of young nodules which had developed for 5 d in the absence of NO ₃ ^- and another 5 d in the presence of 18 mM NO ₃ ^- resembled nodules developing under N-free conditions, except that in the infection threads within the infection zone of the nodule 1) some bacteria tended to loose their normal shape and gain more electron density, indicating premature degradation, and 2) the matrix of the infection threads was abnormally enlarged. In the presence of high NO ₃ ^- levels in the medium, lysis and degeneration of the bacteria released from the infection threads were observed in the infection and bacteroid zones of developing nodules, indicative of premature senescence. On the other hand, the nodule meristems continued to proliferate even after 12 d of exposure of 18 mM NO ₃ ^- . This was the only morphogenetic step of root nodulation which was insensitive to levels of combined nitrogen that completely prevented infection if present at the time of inoculation. These data indicate that all of the recognized steps of root nodule morphogenesis in which the bacteria play a key role are sensitive to the inhibitory effect of combined nitrogen.     

Paleosols and host rocks from the Middle–Upper Permian reference section of the Kazan Volga region,Russia: A case study

The Urzhumian (Wordian) and Severodvinian (Capitanian) reference section of the Monastery Ravine (Kazan Volga region, Russia), contains two siltstone lithofacies: (a) laminated and (b) massive. Depositional settings of the laminated siltstones can be interpreted as perennial to ephemeral lakes; depositional settings of the massive siltstones are interpreted as floodplains with soil cover and periodical silt influx in wet seasons. The bulk geochemistry of siliciclastics has revealed a high degree of weathering of both types of siltstone. The similar chemical composition, mineralogy, and grain size suggest the same provenance of silt material. Geochemical data indicate eastern source rocks, which are the Permian red beds of the Cis-Ural plains.The main genetic types of paleosols hosted in the massive siltstones in the studied section, include moderately developed Vertisols and Calcisols with drab-colored root traces, calcareous nodules, low chroma mottles, angular blocky peds and slickensides. These pedofeatures indicate in general a semi-arid climate with clear seasonality of rainfall. Major oxides of the paleosol matrix were used to estimate paleoprecipitation through the bases to alumina (ΣBases/Al) ratio and chemical index of alteration minus potassium (CIA-K) proxies. Estimates from Urzhumian paleosols indicate relatively low mean annual precipitation (MAP) of 390 mm/yr. The transition to the Severodvinian paleosols is marked by a noticeable MAP increase up to 777 mm/yr. This climate moistening coincides with changes in the morphology of paleosols from dolomitic with low redoximorphy to calcitic with gley horizons. The pedogenic carbonate nodules consisting of dolomicrite (5–10 μm) are very common in the Urzhumian paleosols and their morphology, micromorhology and isotopic features indicate the pedogenic origin of dolomite.Sedimentological and paleopedological features of the studied siltstones, as well as the location of the Volga-Ural basin in a mid-latitude position (25–32 °N) indicate a monsoonal character of precipitation during the Middle Permian.     

Paleoenvironmental reconstruction of middle Miocene paleosols bearing Kenyapithecus and Victoriapithecus, Nyakach Formation, southwestern Kenya

Paleosols in the middle Miocene (15 Ma) Nyakach Formation at Kaimogool, near Sondu, southwestern Kenya have yielded specimens of the early cercopithecoid Victoriapithecus macinnesi and the early kenyapithecine Kenyapithecus africanus, and can be used as evidence for the environmental mosaic occupied by these primates. Five distinct types of paleosols (pedotypes) are recognized in the Nyakach Formation section at Kaimogool South. The most common paleosols are reddish brown, silty calcareous profiles with blocky structure and large root traces (Ratong pedotype) which are interpreted as soils of well-drained, dry bushland or thicket (nyika). Weakly developed paleosols associated with paleochannels (Dhero pedotype) represent wooded grassland early in the ecological succession from streamside flooding. One of these paleosols has yielded a fossil flora of grasses and small-leaved dicots like those of modern semi-arid wooded grassland. Crumb structured, calcareous paleosols with iron-manganese nodules (Yom pedotype) are interpreted to represent seasonally waterlogged, wooded grassland (dambo or vlei). Thick, red clayey, calcareous paleosols with blocky ped structure and large root traces (Tut pedotype) are interpreted as soils of well-drained dry woodland. Other blocky-structured, gray to brown calcareous paleosols with iron-manganese nodules (Chido pedotype) are interpreted as soils of seasonally waterlogged, riparian dry woodland. Fossil soils, plants and gastropods are evidence of an unusually dry (300-500 mm mean annual precipitation) habitat for apes, consisting of a vegetational mosaic dominated by dry woodland, bushland and thickets with few areas of seasonally waterlogged grassland. Fossils of V. macinnesi are rare from Nyakach, but were found in paleosols representative of bushland and thicket habitats (Ratong). Fossils of the ape K. africanus were found within paleosols indicative of dry woodland (Tut). Other paleosol types representative of seasonally dry dambo grassland (Yom), colonizing grassland (Dhero) or riparian woodland (Chido) are also represented, but have not yet produced primate fossils.     

豆科植物根瘤内生细菌的发现及其研究进展

近年来研究报道显示,某些豆科植物与根瘤菌在形成固氮共生体的同时,其根瘤内还存在多种其他类群的内生细菌,该现象在根瘤菌研究领域越来越引起关注和重视。本文综述了根瘤内生土壤杆菌、非共生根瘤菌、其它细菌的发现、种类及其对共生关系和植物生长的影响等研究进展,同时对该研究方向提出一些初步观点和认识,旨在增加人们对根瘤微生态的了解,拓展根瘤菌研究与应用的视野。     

Bacteriology of Manganese Nodules: I. Bacterial Action on Manganese in Nodule Enrichments

Bacteria, found in manganese nodules from the Atlantic Ocean, enhance the adsorption of Mn from sea water by crushed manganese nodules in the presence of peptone. When bacterial outgrowth from crushed manganese nodules was experimentally delayed, peptone did not enhance Mn adsorption by nodular substance, but hindered it in some cases. A mechanism to explain the role of bacteria in enhancing Mn adsorption by manganese nodules is presented. Oyster shells were shown to adsorb Mn in the absence of bacteria. Peptone did not enhance the rate of Mn adsorption. Adsorbed Mn was not visibly oxidized during experimental observation. These results suggest one way whereby nodule formation may be initiated in the oceans. Some bacteria in the nodules were found to release manganese from them in the presence of glucose and peptone. Bacteria may, therefore, play a role not only in nodule buildup but also in nodule breakdown.     

Microbes: Mini Iron Factories

Microbes have flourished in extreme habitats since beginning of the Earth and have played an important role in geological processes like weathering, mineralization, diagenesis, mineral formation and destruction. Biotic mineralization is one of the most fascinating examples of how microbes have been influencing geological processes. Iron oxidizing and reducing bacteria are capable of precipitating wide varieties of iron oxides (magnetite), carbonates (siderite) and sulphides (greigite) via controlled or induced mineralization processes. Microbes have also been considered to play an important role in the history of evolution of sedimentary rocks on Earth from the formation of banded iron formations during the Archean to modern biotic bog iron and ochre deposits. Here, we discuss the role that microbes have been playing in precipitation of iron and the role and importance of interdisciplinary studies in the field of geology and biology in solving some of the major geological mysteries.     

PET-CT在非完全实性肺结节中的应用价值

肺癌在中国恶性肿瘤的发病率位居第一,随着低剂量薄层CT在肺癌筛查中的广泛应用,临床发现更多表现为非完全实性结节的肺腺癌,目前众多研究使CT影像学特征和肺腺癌病理的关系得到更进一步的认知,虽然CT能对部分非完全实性结节做出定性和定位诊断,但仍有部分非完全实性结节诊断困难,PET-CT结合了病灶的代谢信息和精确的定位信息,从而提高对肺部结节诊断的敏感性、特异性、准确性,综合多个文献PET-CT在非完全实性结节中的诊断分期价值较CT无明显提升,却在评估预后和制定合适手术方案上可以起到一定的作用,本文就PET-CT在SSN中的应用价值进行阐述。     

豌豆根瘤中细菌的扫描电镜观察

用扫描电镜观察了豌豆根瘤的侵染细胞.结果表明,在这些细胞中有大量的细菌,它们主要是杆状细菌,其次是球形、Y形和T形细菌,其它形状的细菌很少.除了细菌形状不同外,还有一些细菌比较特殊,如有的细菌较长,菌体出现部分收缩并形成一个或一个以上的收缩环,其形状类似一条莲根;有的细菌很大,它的体积是普通细菌的2倍或2倍以上;有的细菌粗细不均匀,端部膨大,呈棒槌状.侵染细胞中有许多小泡,它们大小不同,呈球形.它们存于细菌之间,其中一些小泡还位于细菌的表面上,而且附近细菌的表面有时还有各种隆起.     

The presence,nature, and role of gut microflora in aquatic invertebrates: A synthesis

This review of the literature concerns the gut microbiota of aquatic invertebrates and highlights the questions and processes that merit attention if an understanding of the role of gut microbes in the physiology of host invertebrates and nutrient dynamics of aquatic systems is to be gained. A substantial number of studies report the presence of gut microbes in aquatic invertebrates. Crustacea, Mollusca, and Echinodermata have received the most attention, with few studies involving other invertebrate groups. Different types of associations (e.g., ingestion, contribution of exoenzymes, incubation, parasitism) are reported to occur between gut microbes and aquatic invertebrates, and it is clear that gut bacterial communities cannot be treated as single functional entities, but that individual populations require examination. In addition, gut microbes may be either ingested transients or residents, the presence of which have different implications for the invertebrate. The most commonly reported genera of gut bacteria are Vibrio, Pseudomonas, Flavobacterium, Micrococcus, and Aeromonas. Quite a number of authors report the physiological properties of gut microbes (including enzyme activities and attributes such as nitrogen fixation), while less attention has been given to consideration of the colonization sites within the digestive tract, the density and turnover of gut bacteria, and the factors affecting the presence and nature of gut microflora. In addition, although a few studies have demonstrated a positive relationship between invertebrates and their gut microbiota, particularly with regard to nutrient gain by the invertebrate, very little conclusive evidence exists as to the role of bacteria in the physiology of host invertebrates. This has resulted from a lack of process-oriented studies. The findings for aquatic gut microbes are compared to those of gut bacteria associated with terrestrial invertebrates, where gut microbes contribute significantly to nutrient gain by the host in some environments.     

Perspectives of plant-associated microbes in heavy metal phytoremediation

"Phytoremediation" know-how to do-how is rapidly expanding and is being commercialized by harnessing the phyto-microbial diversity. This technology employs biodiversity to remove/contain pollutants from the air, soil and water. In recent years, there has been a considerable knowledge explosion in understanding plant-microbes-heavy metals interactions. Novel applications of plant-associated microbes have opened up promising areas of research in the field of phytoremediation technology. Various metabolites (e.g., 1-aminocyclopropane-1-carboxylic acid deaminase, indole-3-acetic acid, siderophores, organic acids, etc.) produced by plant-associated microbes (e.g., plant growth promoting bacteria, mycorrhizae) have been proposed to be involved in many biogeochemical processes operating in the rhizosphere. The salient functions include nutrient acquisition, cell elongation, metal detoxification and alleviation of biotic/abiotic stress in plants. Rhizosphere microbes accelerate metal mobility, or immobilization. Plants and associated microbes release inorganic and organic compounds possessing acidifying, chelating and/or reductive power. These functions are implicated to play an essential role in plant metal uptake. Overall the plant-associated beneficial microbes enhance the efficiency of phytoremediation process directly by altering the metal accumulation in plant tissues and indirectly by promoting the shoot and root biomass production. The present work aims to provide a comprehensive review of some of the promising processes mediated by plant-associated microbes and to illustrate how such processes influence heavy metal uptake through various biogeochemical processes including translocation, transformation, chelation, immobilization, solubilization, precipitation, volatilization and complexation of heavy metals ultimately facilitating phytoremediation.     

Involvement of Microorganisms in the Formation of Carbonate Speleothems in the Cervo Cave (L'Aquila-Italy)

Much is known about the bacterial precipitation of carbonate rocks, but comparatively little is known about the involvement of microbes in the formation of secondary mineral structures in caves. We hypothesized that bacteria isolated from calcareous stalactites, which are able to mediate CaCO₃ precipitation in vitro, play a role in the formation of carbonate speleothems. We collected numerous cultivable calcifying bacteria from calcareous speleothems from Cervo cave, implying that their presence was not occasional. The relative abundance of calcifying bacteria among total cultivable microflora was found to be related to the calcifying activity in the stalactites. We also determined the δ ¹³C and δ ¹⁸ O values of the Cervo cave speleothems from which bacteria were isolated and of the carbonates obtained in vitro to determine whether bacteria were indeed involved in the formation of secondary mineral structures. We identified three groups of biological carbonates produced in vitro at 11°C on the basis of their carbon isotopic composition: carbonates with δ ¹³C values (a) slightly more positive, (b) more negative, and (c) much more negative than those of the stalactite carbonates. The carbonates belonging to the first group, characterized by the most similar δ ¹³C values to stalactites, were produced by the most abundant strains. Most of calcifying isolates belonged to the genus Kocuria. Scanning electron microscopy showed that dominant morphologies of the bioliths were sherulithic with fibrous radiated interiors. We suggest a mechanism of carbonate crystal formation by bacteria.     

Hydrocarbon utilization by nodule bacteria and plant growth-promoting rhizobacteria

Standard and locally isolated nodule bacteria and plant growth-promoting rhizobacteria (PGPR) were grown on crude oil and individual pure hydrocarbons as sole sources of carbon and energy. The nodule bacteria included two standard Rhizobium leguminosarum strains, two standard Bradyrhizobium japonicum strains, and one unknown nodule bacterial strain that was locally isolated from Vicia faba nodules. The PGPR included one standard Serratia liquefaciens strain and two locally isolated strains of Pseudomonas aeruginosa and Flavobacterium sp. The pure hydrocarbons tested included n-alkanes with chain lengths from C9 to C40 and the aromatic hydrocarbons benzene, biphenyle, naphthalene, phenanthrene, and toluene. Quantitative gas liquid chromatographic analyses confirmed that pure cultures of representative nodule bacteria and PGPR could attenuate n-octadecane and phenanthrene in the surrounding nutrient medium. Further, intact nodules of V. faba containing bacteria immobilized on and within those nodules reduced hydrocarbon levels in a medium in which those nodules were shaken. It was concluded that legume crops are suitable phytoremediation tools for oily soil, since they enrich such soils not only with fixed nitrogen, but also with hydrocarbon-utilizing microorganisms. Further, legume nodules may have biotechnological value as materials for cleaning oily liquid wastes.     

Spiders,microbes and sex: Bacterial exposure on copulatory organs alters mating behaviour in funnel‐web spiders

Environmental microbes have the potential to be involved in nearly all behavioural processes. For example, mating systems where males use intromittent organs to transfer sperm to females represent a means by which environmental microbes collected by males can breach entry into females' body cavities during mating. However, the degree to which the acquisition of environmental microbes onto important sex structures alters courtship behaviours remains unknown. Here, we collected bacteria from the copulatory organs of Agelenopsis pennsylvanica funnel‐weaving spiders in situ to test whether exposure to bacteria on copulatory organs can alter hosts' courtship behaviour, reproductive success and survival. We used a standardized assay to repeatedly measure each spider's aggressiveness, a behavioural component of both male courtship and female sexual receptivity. Then, we experimentally altered the bacteria present on male and female spiders' copulatory organs with an application of either (a) a mixture of bacteria collected from conspecifics to increase bacterial presence, (b) an antibiotic to reduce bacterial presence or (c) a procedural control. Each spider was paired with a size‐matched spider of the opposite sex whose copulatory organs were unaltered, and we measured the latency until the onset and the duration of courtship. Spiders were then isolated, and we measured each individual's time until death and female fecundity over the next 40 days. We found that female exposure to bacteria had multiple effects on mating dynamics. Males took over four times longer to begin courting females that had been exposed to bacteria compared to unexposed and antibiotic‐treated females. Only when courting these bacteria‐exposed females, males began courtship sooner when females were more aggressive. Lastly, females whose mate had been exposed to bacteria experienced reduced survival. These data suggest that bacteria present on animals' copulatory organs can alter courtship behaviours, female survivorship, and may potentially play a role in mating dynamics.     

褐家鼠精母细胞中联会复合体的研究Ⅳ.常染色体联会复合体的发育和偶线期节的研究

采用表面铺展-SDS处理、硝酸银和磷钨酸（Phosphotungsticacid,PTA）染色电镜技术,研究了褐家鼠精母细胞中常染色体联会复合体（Synaptonemacomplex,SC）的发育及偶线期节（Zygotenenodule,ZN）。在褐家鼠精母细胞的细线期,常染色体轴心（Axialcores,ACs）已形成,同源轴心在空间上靠近,偶线期SCs开始形成,到粗线期SCs完全形成,于双线期SCs开始解体。在双线期除了个别SCs侧生组分分开外,大多数SCs发生碎片化（fragmentation）．在偶线期未配对的ACs和SCs侧生组分及中央组分上均发现电子密度高的球形或椭圆形的节状结构──偶线期节,ZNss在同源染色体配对过程中起很重要的作用。     

Paleosols,trace fossils,and precipitation estimates of the uppermost Triassic strata in northern New Mexico

This study provides a detailed pedogenic evaluation of two Upper Triassic (Late Norian through Rhaetian) stratigraphic intervals in New Mexico in order to assess the climate and ecology of the Latest Triassic, which ended in a mass extinction. The two study areas are located in north–central and east-central New Mexico and are separated by 200 km. Each section contains abundant paleosols of varying maturity with features that reflect an arid to semiarid climate. There is little pedogenic variation throughout the strata at each location, and a typical paleosol profile is about 1 m thick and has an AB–Bw–Bk–BC horizon succession. Bkm, Bss, Bssk, or Bssg horizons are present in some paleosols. Micromorphological features suggest dominantly well-drained sola (e.g., abundant carbonate nodules, illuviated clay) with minor periods of moist or saturated conditions (e.g., FeMn concretions, FeMn coatings and hypocoatings, sepic-plasmic fabrics). Trace fossils are abundant in these strata and are dominated by Taenidium serpentinum and root traces. Depth-to-carbonate functions estimate that mean annual precipitation was between 200 and 450 +/? 95 mm. Relative to location 1 (eastern New Mexico), location 2 (north–central New Mexico) produced higher paleo-precipitation estimates and has stronger and more abundant sepic-plasmic fabrics in thin sections. The presence of a gleyed paleosol, Camborygma eumnkenomos, and slickensides at location 2 also suggests conditions wetter than at location 1. Taxonomically, all of the paleosols in this study appear to be Entisols or Aridisols and can be grouped into seven representative pedotypes of varying maturity. By comparing these paleosols to modern soils, this study demonstrates that the Late Triassic Western Interior during the Late Norian to Rhaetian was arid to semiarid and supported a desert shrub environment that had localized and periodic moist or saturated soil conditions.     

Paleosols and paleoenvironments of the middle Miocene,Maboko Formation,Kenya

The middle Miocene (15 Ma) Maboko Formation of Maboko Island and Majiwa Bluffs, southwestern Kenya, has yielded abundant fossils of the earliest known cercopithecoid monkey (Victoriapithecus macinnesi), and of a kenyapithecine hominoid (Kenyapithecus africanus), as well as rare proconsuline (Simiolus leakeyorum, cf. Limnopithecus evansi) and oreopithecine apes (Mabokopithecus clarki, M. pickfordi), and galagids (Komba winamensis). Specific habitat preferences can be interpreted from large collections of primate fossils in different kinds of paleosols (pedotypes). Fossiliferous drab-colored paleosols with iron-manganese nodules (Yom pedotype) are like modern soils of seasonally waterlogged depressions (dambo). Their crumb structure and abundant fine root-traces, as well as scattered large calcareous rhizoconcretions indicate former vegetation of seasonally wet, wooded grassland. Other fossiliferous paleosols are evidence of nyika bushland (Ratong), and early-successional riparian woodland (Dhero). No fossils were found in Mogo paleosols interpreted as saline scrub soils. Very shallow calcic horizons (in Yom, Ratong, and Mogo paleosols) and Na-montmorillonite (in Mogo) are evidence of dry paleoclimate (300-500 mm MAP=mean annual precipitation). This is the driest paleoclimate and most open vegetation yet inferred as a habitat for any Kenyan Miocene apes or monkeys. Victoriapithecus was abundant in dambo wooded grassland (Yom) and riparian woodland (Dhero), a distribution like that of modern vervet monkeys. Kenyapithecus ranged through all these paleosols, but was the most common primate in nyika bushland paleosols (Ratong), comparable to baboons and macaques today. Mabokopithecus was virtually restricted to riparian woodland paleosols (Dhero), and Simiolus had a similar, but marginally wider, distribution. Habitat preferences of Mabokopithecus and Simiolus were like those of modern colobus monkeys and mangabeys. A single specimen of Komba was found in dambo wooded grassland paleosol (Yom), a habitat more like that of the living Senegal bushbaby than of rainforest galagids. A shift to non-forest habitats may explain the terrestrial adaptations of Victoriapithecus, basal to the cercopithecid radiation, and of Kenyapithecus, basal to the hominoid radiation. Both taxa are distinct from earlier Miocene arboreal proconsulines, oreopithecines and galagids.     

CERBERUS, a novel U-box protein containing WD-40 repeats, is required for formation of the infection thread and nodule development in the legume–Rhizobium symbiosis

Endosymbiotic infection of legume plants by Rhizobium bacteria is initiated through infection threads (ITs) which are initiated within and penetrate from root hairs and deliver the endosymbionts into nodule cells. Despite recent progress in understanding the mutual recognition and early symbiotic signaling cascades in host legumes, the molecular mechanisms underlying bacterial infection processes and successive nodule organogenesis are still poorly understood. We isolated a novel symbiotic mutant of Lotus japonicus , cerberus , which shows defects in IT formation and nodule organogenesis. Map-based cloning of the causal gene allowed us to identify the CERBERUS gene, which encodes a novel protein containing a U-box domain and WD-40 repeats. CERBERUS expression was detected in the roots and nodules, and was enhanced after inoculation of Mesorhizobium loti . Strong expression was detected in developing nodule primordia and the infected zone of mature nodules. In cerberus mutants, Rhizobium colonized curled root hair tips, but hardly penetrated into root hair cells. The occasional ITs that were formed inside the root hair cells were mostly arrested within the epidermal cell layer. Nodule organogenesis was aborted prematurely, resulting in the formation of a large number of small bumps which contained no endosymbiotic bacteria. These phenotypic and genetic analyses, together with comparisons with other legume mutants with defects in IT formation, indicate that CERBERUS plays a critical role in the very early steps of IT formation as well as in growth and differentiation of nodules.     

Microbial Activity in Caves−A Geological Perspective

Caves are commonly the home of diverse microbial biotas, the sites of active mineral precipitation, and/or receptacles for the deposition of sediment. Mineral precipitation is commonly considered to be abiogenic despite the fact that microbes are present in caves, especially in the twilight zone. Detailed analysis of cave substrates from a geological perspective shows that microbes can mediate constructive (microbe calcification, trapping and binding, mediation of crystal growth) and destructive (substrate etching and breakdown) processes. Potentially these processes can significantly influence the formation and preservation of any cave deposit. Preservation of microbes is possible if mineralization takes place while the microbe is alive or shortly after its demise. If not, all record of the microbe will be lost to decay. Even if the microbes are preserved, it may be difficult to determine if they played an active or passive role in the formation of the deposits in which they are entombed. For old cave deposits, such an assessment must rely on spatial relationships and comparison of textures with those known to form as a result of microbial activity. Nevertheless, available evidence indicates that microbes can play a major role in the formation and modification of cave deposits. Equally, however, it is apparent that the full scope and impact of microbial activity on cave deposits has yet to be realized. Recognition of microbial activity in old CaCO 3 cave deposits relies on (1) documentation and recognition of mineralized microbes, (2) recognition of stromatolitic structures that formed through microbial activity, and/or (3) the identification of fabrics/textures that are known to be indicative of microbial activity. All of these criteria fundamentally rely on the interpretation of fabrics preserved in the cave deposits. Virtually all of these interpretations are open to debate.     

Discovery and structural characterization of a novel glycosidase family of marine origin

The genomic data on heterotrophic marine bacteria suggest the crucial role that microbes play in the global carbon cycle. However, the massive presence of hypothetical proteins hampers our understanding of the mechanisms by which this carbon cycle is carried out. Moreover, genomic data from marine microorganisms are essentially annotated in the light of the biochemical knowledge accumulated on bacteria and fungi which decompose terrestrial plants. However marine algal polysaccharides clearly differ from their terrestrial counterparts, and their associated enzymes usually constitute novel protein families. In this study, we have applied a combination of bioinformatics, targeted activity screening and structural biology to characterize a hypothetical protein from the marine bacterium Zobellia galactanivorans, which is distantly related to GH43 family. This protein is in fact a 1,3-α-3,6-anhydro-l-galactosidase (AhgA) which catalyses the last step in the degradation pathway of agars, a family of polysaccharides unique to red macroalgae. AhgA adopts a β-propeller fold and displays a zinc-dependent catalytic machinery. This enzyme is the first representative of a new family of glycoside hydrolases, especially abundant in coastal waters. Such genes of marine origin have been transferred to symbiotic microbes associated with marine fishes, but also with some specific human populations.