Protein-based phylogenies support a chimeric origin for the eukaryotic genome

The phylogenetic position of the archaebacteria and the place of eukaryotes in the history of life remain a question of debate. Recent studies based on some protein-sequence data have obtained unusual phylogenies for these organisms. We therefore collected the protein sequences that were available with representatives from each of the major forms of life: the gram-negative bacteria, gram-positive bacteria, archaebacteria, and eukaryotes. Monophyletic, unrooted phylogenies based on these sequence data show that seven of 24 proteins yield a significant gram-positive-archaebacteria clade/gram-negative- eukaryotic clade. The phylogenies for these seven proteins cannot be explained by the traditional three-way split of the eukaryotes, archaebacteria, and eubacteria. Nine of the 24 proteins yield the traditional gram-positive-gram-negative clade/archaebacteria-eukaryotic clade. The remaining eight proteins give phylogenies that cannot be statistically distinguished. These results support the hypothesis of a chimeric origin for the eukaryotic cell nucleus formed from the fusion of an archaebacteria and a gram-negative bacteria.      

Dimorphism in methane seep-dwelling ecotypes of the largest known bacteria

We present evidence for a dimorphic life cycle in the vacuolate sulfide-oxidizing bacteria that appears to involve the attachment of a spherical Thiomargarita-like cell to the exteriors of invertebrate integuments and other benthic substrates at methane seeps. The attached cell elongates to produce a stalk-like form before budding off spherical daughter cells resembling free-living Thiomargarita that are abundant in surrounding sulfidic seep sediments. The relationship between the attached parent cell and free-living daughter cell is reminiscent of the dimorphic life modes of the prosthecate Alphaproteobacteria, but on a grand scale, with individual elongate cells reaching nearly a millimeter in length. Abundant growth of attached Thiomargarita-like bacteria on the integuments of gastropods and other seep fauna provides not only a novel ecological niche for these giant bacteria, but also for animals that may benefit from epibiont colonization.     

Survivability of Bacteria Ejected from Icy Surfaces after Hypervelocity Impact

Both the Saturnian and Jovian systems contain satellites with icy surfaces. If life exists on any of these icy bodies (in putative subsurface oceans for example) then the possibility exists for transfer of life from icy body to icy body. This is an application of the idea of Panspermia, wherein life migrates naturally through space. A possible mechanism would be that life,here taken as bacteria, could become frozen in the icy surface ofone body. If a high-speed impact occurred on that surface, ejectacontaining the bacteria could be thrown into space. It could thenmigrate around the local region of space until it arrived at a second icy body in another high-speed impact. In this paper we consider some of the necessary steps for such a process to occur,concentrating on the ejection of ice bearing bacteria in the initial impact, and on what happens when bacteria laden projectiles hit an icy surface. Laboratory experiments using high-speed impacts with a light gas gun show that obtaining icy ejecta with viable bacterial loads is straightforward. In addition to demonstrating the viability of the bacteria carried on the ejecta, we have also measured the angular and size distribution of the ejecta produced in hypervelocity impacts on ice. We have however been unsuccessful at transferring viablebacteria to icy surfaces from bacteria laden projectilesimpacting at hypervelocities.     

黄海日照海域部分可培养细菌的分离、初步鉴定及产琼胶酶细菌的筛选

海洋细菌在海洋的物质与能量循环中起着非常重要的作用。为了适应复杂多变的海洋环境,海洋细菌在物种和基因方面表现出极高的丰富度。[目的] 对中国黄海日照海域部分可培养细菌进行分离、初步鉴定,同时筛选产琼胶酶菌株。[方法] 对从日照海域河流入海口和潮间带沙样和海水中分离到的73株细菌进行了16S rRNA基因序列测定,并进行序列同源性分析。同时检测了这些菌株对琼脂的降解能力。[结果] 结果显示,分离到的73株细菌属于4个门、13个科、34个属。18株细菌可能是新分类单元,其中16株为潜在新种,2株为可能的新属。73株细菌中,5株菌具有降解琼脂的能力,最高的琼胶酶活可达到2.17±0.04 U/mL,其中4株嗜琼胶属的细菌降解琼脂糖的产物均为新琼四糖。[结论] 本研究丰富了人们对黄海海域可培养细菌多样性的理解,为新物种和新酶的研究提供了基础,并为琼胶酶的提取提供了高产菌株。     

Nocturnal production of endospores in natural populations of epulopiscium-like surgeonfish symbionts

Prior studies have described a morphologically diverse group of intestinal microorganisms associated with surgeonfish. Despite their diversity of form, 16S rRNA gene surveys and fluorescent in situ hybridizations indicate that these bacteria are low-G+C gram-positive bacteria related to Epulopiscium spp. Many of these bacteria exhibit an unusual mode of reproduction, developing multiple offspring intracellularly. Previous reports have suggested that some Epulopiscium-like symbionts produce dormant or phase-bright intracellular offspring. Close relatives of Epulopiscium, such as Metabacterium polyspora and Clostridium lentocellum, are endospore-forming bacteria, which raises the possibility that the phase-bright offspring are endospores. Structural evidence and the presence of dipicolinic acid demonstrate that phase-bright offspring of Epulopiscium-like bacteria are true endospores. In addition, endospores are formed as part of the normal daily life cycle of these bacteria. In the populations studied, mature endospores were seen only at night and the majority of cells in a given population produced one or two endospores per mother cell. Phylogenetic analyses confirmed the close relationship between the endospore-forming surgeonfish symbionts characterized here and previously described Epulopiscium spp. The broad distribution of endospore formation among the Epulopiscium phylogenetic group raises the possibility that sporulation is a characteristic of the group. We speculate that spore formation in Epulopiscium-like symbionts may be important for dispersal and may also enhance survival in the changing conditions of the fish intestinal tract.     

Bacteria abundance and diversity of different life stages of Plutella xylostella (Lepidoptera: Plutellidae), revealed by bacteria culture‐dependent and PCR‐DGGE methods

Microbial abundance and diversity of different life stages (fourth instar larvae, pupae and adults) of the diamondback moth, Plutella xylostella L., collected from field and reared in laboratory, were investigated using bacteria culture‐dependent method and PCR‐DGGE analysis based on the sequence of bacteria 16S rRNA V3 region gene. A large quantity of bacteria was found in all life stages of P. xylostella. Field population had higher quantity of bacteria than laboratory population, and larval gut had higher quantity than pupae and adults. Culturable bacteria differed in different life stages of P. xylostella. Twenty‐five different bacterial strains were identified in total, among them 20 strains were presented in larval gut, only 8 strains in pupae and 14 strains in adults were detected. Firmicutes bacteria, Bacillus sp., were the most dominant species in every life stage. 15 distinct bands were obtained from DGGE electrophoresis gel. The sequences blasted in GenBank database showed these bacteria belonged to six different genera. Phylogenetic analysis showed the sequences of the bacteria belonged to the Actinobacteri, Proteobacteria and Firmicutes. Serratia sp. in Proteobacteria was the most abundant species in larval gut. In pupae, unculturable bacteria were the most dominant species, and unculturable bacteria and Serratia sp. were the most dominant species in adults. Our study suggested that a combination of molecular and traditional culturing methods can be effectively used to analyze and to determine the diversity of gut microflora. These known bacteria may play important roles in development of P. xylostella.     

Resolving Nonstop Translation Complexes Is a Matter of Life or Death

Problems during gene expression can result in a ribosome that has translated to the 3′ end of an mRNA without terminating at a stop codon, forming a nonstop translation complex. The nonstop translation complex contains a ribosome with the mRNA and peptidyl-tRNA engaged, but because there is no codon in the A site, the ribosome cannot elongate or terminate the nascent chain. Recent work has illuminated the importance of resolving these nonstop complexes in bacteria. Transfer-messenger RNA (tmRNA)-SmpB specifically recognizes and resolves nonstop translation complexes in a reaction known as trans-translation. trans-Translation releases the ribosome and promotes degradation of the incomplete nascent polypeptide and problematic mRNA. tmRNA and SmpB have been found in all bacteria and are essential in some species. However, other bacteria can live without trans-translation because they have one of the alternative release factors, ArfA or ArfB. ArfA recruits RF2 to nonstop translation complexes to promote hydrolysis of the peptidyl-tRNAs. ArfB recognizes nonstop translation complexes in a manner similar to tmRNA-SmpB recognition and directly hydrolyzes the peptidyl-tRNAs to release the stalled ribosomes. Genetic studies indicate that most or all species require at least one mechanism to resolve nonstop translation complexes. Consistent with such a requirement, small molecules that inhibit resolution of nonstop translation complexes have broad-spectrum antibacterial activity. These results suggest that resolving nonstop translation complexes is a matter of life or death for bacteria.     

Distant interactions in bacteria

Exchange of information between bacteria via physical signals, referred to as “distant interactions” (DI), is the subject of this review. All cases of DI reported to date are discussed, as well as the history of these studies and the place of DI in bacterial communication. Bacterial DI are a particular case of DI occurring in nature (in plants, animals, and fungi). Along with the chemical signals of intracellular communications, DI play a significant role in the life of microorganisms, especially during critical and transitional periods.     

Two functionally distinctive phosphopantetheinyl transferases from amoeba Dictyostelium discoideum

The life cycle of Dictyostelium discoideum is proposed to be regulated by expression of small metabolites. Genome sequencing studies have revealed a remarkable array of genes homologous to polyketide synthases (PKSs) that are known to synthesize secondary metabolites in bacteria and fungi. A crucial step in functional activation of PKSs involves their post-translational modification catalyzed by phosphopantetheinyl transferases (PPTases). PPTases have been recently characterized from several bacteria; however, their relevance in complex life cycle of protozoa remains largely unexplored. Here we have identified and characterized two phosphopantetheinyl transferases from D. discoideum that exhibit distinct functional specificity. DiAcpS specifically modifies a stand-alone acyl carrier protein (ACP) that possesses a mitochondrial import signal. DiSfp in contrast is specific to Type I multifunctional PKS/fatty acid synthase proteins and cannot modify the stand-alone ACP. The mRNA of two PPTases can be detected during the vegetative as well as starvation-induced developmental pathway and the disruption of either of these genes results in non-viable amoebae. Our studies show that both PPTases play an important role in Dictyostelium biology and provide insight into the importance of PPTases in lower eukaryotes.     

Haloalkaliphilic sulfur-oxidizing bacteria in soda lakes

The existence of chemolithoautotrophic sulfur-oxidizing bacteria (SOB) capable of growth in an extremely alkaline and saline environment has not been recognized until recently. Extensive studies of saline, alkaline (soda) lakes located in Central Asia, Africa and North America have now revealed the presence, at relatively high numbers, of a new branch of obligately autotrophic SOB in these doubly extreme environments. Overall more than 100 strains were isolated in pure culture. All of them have the potential to grow optimally at around pH 10 in media strongly buffered with sodium carbonate/bicarbonate and cannot grow at pH<7.5 and Na(+) concentration <0.2 M. The majority of the isolates fell into two distinct groups with differing phylogeny and physiology, that have been described as two new genera in the Gammaproteobacteria; Thioalkalimicrobium and Thioalkalivibrio. The third genus, Thioalkalispira, contains a single obligate microaerophilic species T. microaerophila. The Thioalkalimicrobium group represents a typical opportunistic strategy, including highly specialized, relatively fast-growing and low salt-tolerant bacteria, dominating in hyposaline steppe soda lakes of Central Asia. The genus Thioalkalivibrio includes mostly slowly growing species better adapted to life in hypersaline conditions and with a more versatile metabolism. It includes denitrifying, thiocyanate-utilizing and facultatively alkaliphilic species.     

Bacterial endosymbioses in Solemya (Mollusca: Bivalvia)—Model systems for studies of symbiont–host adaptation

Endosymbioses between chemosynthetic bacteria and marine invertebrates are remarkable biological adaptations to life in sulfide-rich environments. In these mutualistic associations, sulfur-oxidizing chemoautotrophic bacteria living directly within host cells both aid in the detoxification of toxic sulfide and fix carbon to support the metabolic needs of the host. Though best described for deep-sea vents and cold seeps, these symbioses are ubiquitous in shallow-water reducing environments. Indeed, considerable insight into sulfur-oxidizing endosymbioses in general comes from detailed studies of shallow-water protobranch clams in the genus Solemya. This review highlights the impressive body of work characterizing bacterial symbiosis in Solemya species, all of which are presumed to harbor endosymbionts. In particular, studies of the coastal Atlantic species Solemya velum and its larger Pacific congener Solemya reidi are the foundation for our understanding of the metabolism and physiology of marine bivalve symbioses, which are now known to occur in five families. Solemya velum, in particular, is an excellent model organism for symbiosis research. This clam can be collected easily from coastal eelgrass beds and maintained in laboratory aquaria for extended periods. In addition, the genome of the S. velum symbiont is currently being sequenced. The integration of genomic data with additional experimental analyses will help reveal the molecular basis of the symbiont–host interaction in Solemya, thereby complementing the wide array of research programs aimed at better understanding the diverse relationships between bacterial and eukaryotic cells.     

Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics

The availability of complete genome sequences of cellular life forms creates the opportunity to explore the functional content of the genomes and evolutionary relationships between them at a new qualitative level. With the advent of these sequences, the construction of a minimal gene set sufficient for sustaining cellular life and reconstruction of the genome of the last common ancestor of bacteria, eukaryotes, and archaea become realistic, albeit challenging, research projects. A version of the minimal gene set for modern-type cellular life derived by comparative analysis of two bacterial genomes, those of Haemophilus influenzae and Mycoplasma genitalium, consists of ∼250 genes. A comparison of the protein sequences encoded in these genes with those of the proteins encoded in the complete yeast genome suggests that the last common ancestor of all extant life might have had an RNA genome.     

Laboratory Investigation of Ecological Factors Influencing the Environmental Presence of Burkholderia pseudomallei

Factors like temperature, pH value, water content in soil, and ultraviolet rays that might have influence on the survival of environmental Burkholderia pseudomallei strains were evaluated. Data showed that the optimal temperature and pH value for B. pseudomallei were 24 C to 32 C and 5 to 8, respectively. Water content in soil of less than 10% brought about the death of the bacteria within 70 days, while water content of more than 40% maintained bacteria life for 726 days. The bacteria were easily killed by ultraviolet rays at 465 μW/cm² for 7.75 min while other permanent soil bacteria were killed at 1,860 μW/cm² for 31 min. From these results, it could be concluded that proper temperature, enough water in soil, and suitable soil pH might be the three major ecological conditions governing the environmental presence of B. pseudomallei.     

‘Follow the Water’: Hydrogeochemical Constraints on Microbial Investigations 2.4 km Below Surface at the Kidd Creek Deep Fluid and Deep Life Observatory

Abstract

Microbiological and geochemical data are presented to characterize the hydrogeochemistry and to investigate extant microbial life in fracture waters 2.4?km below surface, at the Kidd Creek Observatory in Canada. Previous studies identified the world’s oldest groundwaters with mean residence times on the order of millions to billions of years trapped in fractures in Precambrian host rock here. In this study, major ion chemistry, δ¹⁸O and δ²H isotopic signatures and dissolved gases in the fracture waters are shown to be distinct from potential contamination end-members, demonstrating the fracture waters are not impacted by waters used in mining operations. A previous work on sulfur isotope signatures suggested a longstanding indigenous population of sulfate-reducing bacteria in these highly reducing fluids and sufficient sulfate to support microbial activity. Here, we report the first evidence for extant visible and cultivable microbial life at this location. Anaerobic metabolisms were investigated using the Most Probable Number (MPN) method. The fracture fluids contained extant cells at low biomass density (～10³–10⁴ cells/mL) and showed a strong response from autotrophic sulfate-reducers and alkane-oxidizing sulfate reducers. These lines of evidence provide the interpretational framework (chemical, hydrogeologic, and microbiologic) essential to the on-going genomic and metagenomic investigations at the Kidd Creek Observatory – the world’s most longstanding location for investigation of subsurface fluids and deep life at such profound depth.     

A descriptive analysis of gut microbiota composition in differentially reared infant rhesus monkeys (Macaca mulatta) across the first 6 months of life

The gastrointestinal microbiome is recognized as a critical component in host immune function, physiology, and behavior. Early life experiences that alter diet and social contact also influence these outcomes. Despite the growing number of studies in this area, no studies to date have examined the contribution of early life experiences on the gut microbiome in infants across development. Such studies are important for understanding the biological and environmental factors that contribute to optimal gut microbial colonization and subsequent health. We studied infant rhesus monkeys (Macaca mulatta) across the first 6 months of life that were pseudo‐randomly assigned to one of two different rearing conditions at birth: mother‐peer‐reared (MPR), in which infants were reared in social groups with many other adults and peers and nursed on their mothers, or nursery‐reared (NR), in which infants were reared by human caregivers, fed formula, and given daily social contact with peers. We analyzed the microbiome from rectal swabs (total N = 97; MPR = 43, NR = 54) taken on the day of birth and at postnatal Days 14, 30, 90, and 180 using 16S rRNA gene sequencing. Bacterial composition differences were evident as early as 14 days, with MPR infants exhibiting a lower abundance of Bifidobacterium and a higher abundance of Bacteroides than NR infants. The most marked differences were observed at 90 days, when Bifidobacterium, Lactobacillus, Streptococcus, Bacteroides, Clostridium, and Prevotella differed across rearing groups. By Day 180, no differences in the relative abundances of the bacteria of interest were observed. These novel findings in developing primate neonates indicate that the early social environment as well as diet influence gut microbiota composition very early in life. These results also lay the groundwork for mechanistic studies examining the effects of early experiences on gut microbiota across development with the ultimate goal of understanding the clinical significance of developmental changes.     

植物相关细菌中Ⅵ型分泌系统的功能研究进展北大核心

型分泌系统(typeⅥsecretion system,T6SS)是一种强大的细菌分子武器,它通过将效应蛋白注入原核或真核细胞而介导细菌间竞争并影响宿主的生命活动。T6SS广泛分布于革兰氏阴性菌中,主要存在于变形菌门(Proteobacteria)。尽管T6SS的研究大多集中在动物相关细菌上,但它在植物相关细菌中的作用不能被忽视。本文对植物相关细菌的T6SS进行了较为详细的介绍,主要从T6SS的发现、T6SS在植物相关细菌间竞争中的作用、在细菌与植物互作中的作用以及在植物生物防治中的作用等4个方面综述了最新的研究成果,旨在为今后更好地研究植物相关细菌T6SS的生物学功能及其应用提供指导。     

Molecular battle between host and bacterium: recognition in innate immunity

During infection, our innate immune system is the first line of defense and has evolved to clear invading bacteria immediately. To do so, recognition is the key element. However, how does the innate immune system distinguish self from nonself, and how does it recognize all bacteria (estimated to be far over a million species)? The answer lies in the recognition of evolutionary conserved structures. In this review, we approach this phenomenon from the bacterial perspective. What are the evolutionary conserved structures in bacteria, and what strategies are there in the human innate immune system to sense these structures? We illustrate most examples both at the functional as well as at the molecular level. Furthermore, we highlight how pathogenic bacteria can evade this recognition to survive better in the human host which in turn can result in life‐threatening diseases. Copyright © 2011 John Wiley & Sons, Ltd.