Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments

The oxidation of methane in anoxic marine sediments is thought to be mediated by a consortium of methane-consuming archaea and sulfate-reducing bacteria. In this study, we compared results of rRNA gene (rDNA) surveys and lipid analyses of archaea and bacteria associated with methane seep sediments from several different sites on the Californian continental margin. Two distinct archaeal lineages (ANME-1 and ANME-2), peripherally related to the order Methanosarcinales, were consistently associated with methane seep marine sediments. The same sediments contained abundant (13)C-depleted archaeal lipids, indicating that one or both of these archaeal groups are members of anaerobic methane-oxidizing consortia. (13)C-depleted lipids and the signature 16S rDNAs for these archaeal groups were absent in nearby control sediments. Concurrent surveys of bacterial rDNAs revealed a predominance of delta-proteobacteria, in particular, close relatives of Desulfosarcina variabilis. Biomarker analyses of the same sediments showed bacterial fatty acids with strong (13)C depletion that are likely products of these sulfate-reducing bacteria. Consistent with these observations, whole-cell fluorescent in situ hybridization revealed aggregations of ANME-2 archaea and sulfate-reducing Desulfosarcina and Desulfococcus species. Additionally, the presence of abundant (13)C-depleted ether lipids, presumed to be of bacterial origin but unrelated to ether lipids of members of the order Desulfosarcinales, suggests the participation of additional bacterial groups in the methane-oxidizing process. Although the Desulfosarcinales and ANME-2 consortia appear to participate in the anaerobic oxidation of methane in marine sediments, our data suggest that other bacteria and archaea are also involved in methane oxidation in these environments.     

Molecular characterization of polychlorinated biphenyl-dechlorinating populations in contaminated sediments

Polychlorinated biphenyl (PCB)-dechlorinating microorganisms were characterized in PCB-contaminated sediments using amplified ribosomal DNA restriction analysis (ARDRA). The sediments were prepared by spiking Aroclor 1248 into PCB-free sediments, and were inoculated with microorganisms eluted from St. Lawrence River sediments. PCB-free sediments inoculated with the same inoculum served as the control. Four restriction fragment length polymorphism (RFLP) groups in the eubacterial and two in the archaeal domain were found exclusively in PCB-spiked sediment clone libraries. Sequence analysis of the four eubacterial clones showed homology to Escherichia coli, Lactosphaera pasteurii, Clostridium thermocellum, and Dehalobacter restrictus. The predominant archaeal sequence in the PCB-spiked sediment clone library was closely related to Methanosarcina barkeri, which appear to support earlier findings that methanogens are involved in PCB dechlorination. When the dot-blot hybridization was performed between the sediment DNA extract and the probes designed with eubacterial RFLP groups, the intensity of two of eubacterial RFLP groups, which showed high sequence homology to C. pascui and D. restrictus, was highly correlated with the number of dechlorinating microorganisms suggesting these two members intend to contribute to PCB dechlorination.     

Comparative Analysis of Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in Anoxic Marine Sediments

The oxidation of methane in anoxic marine sediments is thought to be mediated by a consortium of methane-consuming archaea and sulfate-reducing bacteria. In this study, we compared results of rRNA gene (rDNA) surveys and lipid analyses of archaea and bacteria associated with methane seep sediments from several different sites on the Californian continental margin. Two distinct archaeal lineages (ANME-1 and ANME-2), peripherally related to the order Methanosarcinales, were consistently associated with methane seep marine sediments. The same sediments contained abundant ¹³C-depleted archaeal lipids, indicating that one or both of these archaeal groups are members of anaerobic methane-oxidizing consortia. ¹³C-depleted lipids and the signature 16S rDNAs for these archaeal groups were absent in nearby control sediments. Concurrent surveys of bacterial rDNAs revealed a predominance of δ-proteobacteria, in particular, close relatives of Desulfosarcina variabilis. Biomarker analyses of the same sediments showed bacterial fatty acids with strong ¹³C depletion that are likely products of these sulfate-reducing bacteria. Consistent with these observations, whole-cell fluorescent in situ hybridization revealed aggregations of ANME-2 archaea and sulfate-reducing Desulfosarcina and Desulfococcus species. Additionally, the presence of abundant ¹³C-depleted ether lipids, presumed to be of bacterial origin but unrelated to ether lipids of members of the order Desulfosarcinales, suggests the participation of additional bacterial groups in the methane-oxidizing process. Although the Desulfosarcinales and ANME-2 consortia appear to participate in the anaerobic oxidation of methane in marine sediments, our data suggest that other bacteria and archaea are also involved in methane oxidation in these environments.     

The biodiversity of macrofaunal organisms in marine sediments

Marine sediments cover most of the ocean bottom, and the organisms that reside in these sediments therefore constitute the largest faunal assemblage on Earth in areal coverage. The biomass in these sediments is dominated by macrofauna, a grouping of invertebrate polychaetes, molluscs, crustaceans and other phyla based on size. Globally, only a small portion of marine habitats have been sampled for macrofauna, but sampled areas have led to global estimates of macrofaunal species number ranging from 500,000 to 10,000,000. Most of these species are undescribed, and global syntheses of patterns of individual taxa and biodiversity are few and based on limited samples. The significance of biodiversity in marine sediments to ecosystem processes is poorly understood, but individual species and functional groups are known to carry out activities that have global importance. Macrofaunal activity impacts global carbon, nitrogen and sulphur cycling, transport, burial and metabolism of pollutants, secondary production including commercial species, and transport of sediments. Documented extinctions of marine macrofauna are few, but the ramifications of species loss through habitat shrinkage and undocumented extinctions are unknown. Limited data suggest there is substantial functional redundancy in macrofauna within trophic groups but whether this redundancy is sufficient to allow species loss without significantly altering ecosystem processes is unknown. Sorely needed are experiments that test specific hypotheses on biodiversity, redundancy, and ecosystem processes as they relate to marine macrofauna.     

Functional gene groups are concentrated within chromosomes,among chromosomes and in the nuclear space of the human genome

Genomes undergo changes in organization as a result of gene duplications, chromosomal rearrangements and local mutations, among other mechanisms. In contrast to prokaryotes, in which genes of a common function are often organized in operons and reside contiguously along the genome, most eukaryotes show much weaker clustering of genes by function, except for few concrete functional groups. We set out to check systematically if there is a relation between gene function and gene organization in the human genome. We test this question for three types of functional groups: pairs of interacting proteins, complexes and pathways. We find a significant concentration of functional groups both in terms of their distance within the same chromosome and in terms of their dispersal over several chromosomes. Moreover, using Hi-C contact map of the tendency of chromosomal segments to appear close in the 3D space of the nucleus, we show that members of the same functional group that reside on distinct chromosomes tend to co-localize in space. The result holds for all three types of functional groups that we tested. Hence, the human genome shows substantial concentration of functional groups within chromosomes and across chromosomes in space.     

Siboglinid evolution shaped by habitat preference and sulfide tolerance

Siboglinids are tube-dwelling annelids that inhabit marine reducing habitats such as anoxic mud bottoms, seeps and hydrothermal vents. As adults, they lack a functional digestive system and rely on chemoautotrophic microbial endosymbionts. Based on morphological analyses, Siboglinidae form a clade with the Sabellariidae, Serpulidae and Sabellidae within the Annelida. The sister group to this clade is the Oweniidae. Three subgroups constitute the Siboglinidae: Frenulata typically inhabit anoxic sediments, Sclerolinium (a.k.a., Monilifera) live on decaying organic matter or reduced sediments and Vestimentifera are mostly found at hydrocarbon seeps and hydrothermal vents. Recent studies suggest that Sclerolinum is the sister group to the Vestimentifera. Within the Vestimentifera, the species inhabiting bare-rock hydrothermal vents represent a derived clade. The seep-inhabiting genus Lamellibrachia forms a basal branch within the Vestimentifera. Trends in siboglinid evolution are most notable with regard to the level of sulfide tolerance and type of substrate. Basal groups inhabit soft substrate with only slightly elevated sulfide levels, whereas more derived species colonize hard substrate and tolerate elevated temperatures and high levels of sulfide. The type of substrate correlates with tube morphology and the function of the opisthosome. The role of the symbionts in habitat selection needs further investigation.     

Mobility of iron in the estuaries of the Rhine and the Ems relevant to plant-availability problems

Studies were undertaken to obtain information on the iron mobilization processes in the sediments of the rivers Rhine and Ems, both located in western Europe. On their way from the fresh-water tidal area to the marine environment these sediments loose a considerable amount of their iron. The iron is released from the sediment by means of biodegradation products of the organic matter which dissolve the iron as organic iron complexes. The major functional groups of these organic compounds responsible for the iron mobilization are carboxyls and phenolic hydroxyls. From the sediments of the river Ems greater amounts of organic iron compounds are dissolved than from sediments of the river Rhine. Also fewer organic compounds are released from marine sediments than from fresh-water sediments, which indicates a diminished iron mobility in the marine area of the delta. Besides this the organic compounds from the marine sediments show an impoverishment in their functional groups. The sediments of the rivers Rhine and Ems are also distinguished by a different occupation of functional groups in the organic compounds. On account of a number of experiments the mobilization capacity of these river systems have been discussed.From a viewpoint of plant nutrition the mobility of iron in deposits of different ripening stages was also investigated.     

Recognition of family-specific calls in stripe-backed wrens

Males of the cooperatively breeding stripe-backed wren Campylorhynchus nuchalis, learn repertoires of stereotyped calls (termed WAY calls) from older male relatives. As a result, these vocalizations are normally specific to patrilineal family groups but are sometimes shared by male relatives in different groups. To determine whether or not this species can recognize the calls of different family groups, I performed playback experiments with individual call types recorded from males of known social and genealogical relationships. Subjects discriminated between the calls of unrelated neighbouring groups and unfamiliar groups, and they discriminated both of these from calls of their own groups. However, subjects failed to distinguish calls of males in other groups from calls of their own groups when these males were members of the same patriline. These results indicate that stripe-backed wrens can discriminate between repertoires of these calls that match or differ from their own. Consequently, they can recognize members of their patriline, not just members of their immediate group. These vocalizations probably provide a useful mechanism for recognizing group membership in this species and might also provide a mechanism for recognizing unfamiliar relatives in other groups. Copyright 1999 The Association for the Study of Animal Behaviour.     

Inventory of the benthic eukaryotic diversity in the oldest European lake

We have profound knowledge on biodiversity on Earth including plants and animals. In the recent decade, we have also increased our understanding on microorganisms in different hosts and the environment. However, biodiversity is not equally well studied among different biodiversity groups and Earth''s systems with eukaryotes in freshwater sediments being among the least known. In this study, we used high‐throughput sequencing of the 18S rRNA gene to investigate the entire diversity of benthic eukaryotes in three distinct habitats (littoral sediment and hard substrate, profundal sediment) of Lake Ohrid, the oldest European lake. Eukaryotic sequences were dominated by annelid and arthropod animals (54% of all eukaryotic reads) and protists (Ochrophyta and Ciliophora; together 40% of all reads). Eukaryotic diversity was 15% higher in the deep profundal than on either near‐surface hard substrates or littoral sediments. The three habitats differed in their taxonomic and functional community composition. Specifically, heterotrophic organisms accounted for 92% of the reads in the profundal, whereas phototrophs accounted for 43% on the littoral hard substrate. The profundal community was the most homogeneous, and its network was the most complex, suggesting its highest stability among the sampled habitats.     

浑河流域大型底栖动物摄食功能群对栖息地环境的选择适应性

在生态系统中特定的环境变量组合对应着特定的物种群落结构。栖息地环境的不同,大型底栖动物的分布和所表现出的生物学特征也存在差异。在浑河流域选取22个点位进行调查研究,通过对大型底栖动物进行功能群分类并结合生物性状分析(BTA, Biological Traits Analysis)对浑河流域不同大型底栖动物摄食功能群对栖息地生境的选择适应性进行研究。研究结果表明:捕食者功能群主要以毛翅目为主;直接收集者功能群主要以双翅目为主;刮食者功能群主要以基眼目为主;过滤收集者多为颤蚓目。浑河流域不同大型底栖动物摄食功能群存在明显的空间差异,典范对应分析结果显示:影响捕食者功能群的驱动因子是流速,直接收集者功能群的驱动因子是IOS指数,刮者功能群的驱动因子是溶解氧;过滤收集者功能群的驱动因子是溶解氧和电导率。生物性状分析结果显示:捕食者功能群身体上附有一层硬壳保护,可在水体中自由活动,多分布流速较快,底质复杂的小鹅卵石、圆石的底质中;直接收集者只有头壳具有较厚的甲壳质壁,头部口器不能直接摄食,所以多以微粒有机颗粒为主,分布在石块、部分圆石以及部分粗砂中;刮食者多以藻类、菌类等为食,足腺多分泌粘液,多粘附在较深流速缓慢,底质多为细沙粗粒,食物来源充足的水体;过滤收集者喜栖于淤泥底质中,吸食淤泥或过滤有机碎屑,故多分布于淤泥与细沙底质中。     

Intragroup cohesion and intergroup hostility: the relation between grooming distributions and intergroup competition among female primates

In some primate species, females interact affinitively withmany related and unrelated females, whereas in other speciesfemales interact with only a small subset of available partners.One explanation for high rates of affinitive interactions amongfemale members of the same group is that they function to maintainthe group's cohesion in competition for resources against othergroups. Here, I attempt to determine if grooming is more "egalitarian"or diverse in groups that compete aggressively with their neighborsthan in groups in which females rarely take an active role inbetween-group competition. Three types of data are considered.The first concerns grooming and intergroup encounters in onepopulation of free-ranging vervet monkeys. The second concernsgrooming interactions in a captive population of vervets beforeand after females in adjacent cages began to respond aggressivelyto one another. The third involves a literature survey of avariety of species. When only female-bonded species are considered,there is no relation between the diversity of grooming withingroups and female participationin intergroup encounters. Therealso appears to be no clear relation between the strength ofthe female dominance hierarchy and the diversity of groomingamong females. Female-bonded groups are apparently composedof subgroups allied in a loose confederation against other groups.Female members of the same group may compete against other groupsas a cohesive unit, but their grooming relationships are oftensharply differentiated.     

The ethics of functional genomics: same, same, but different?

Respect for human life--a notion of worth uniting all members of the human race--constitutes a sense of anthropocentrism that has long been the justification for the enrollment of animals in experimentation executed to develop therapies to alleviate human suffering. Currently, however, advances in functional genomics are causing a qualitative transformation of the rationale for medical research performed on animals. The notion of human distinctness is being fundamentally challenged when gene sequences similar to those found in humans are identified in different species. In this Opinion article, we would like to highlight an inherent tension brought about by the current developments in functional genomics: a tension between the scientific and the ethical status of gene sequences. Is it reasonable to argue that they are the same for all practical purposes but different in ethical status?     

Structural insights into group II TRP channels

The seven members of the TRP channel superfamily are divided into two main groups with five members comprising group I (TRPC/V/M/N/A) and TRPML (TRP MucoLipin) and TRPP (TRP Polycystin) making up group II. Group II channels share a high sequence homology on their transmembrane domains and are distinct from group I members as they contain a large luminal/extracellular domain between transmembrane helix 1 (S1) and S2. Since 2016, there are more than ten research papers reporting various structures of group II channels by either cryo-EM or X-ray crystallography. These studies along with recent functional analysis by the other groups have considerably strengthened our knowledge on TRPML and TRPP channels. In this review, we summarize and discuss these reports providing molecular insights into the group II TRP channel family.     

Migratory charr schools exhibit population and kin associations beyond juvenile stages

Few studies have critically investigated the genetic composition of wild fish schools. Yet, such investigations may have profound implications for the understanding of social organization and population differentiation in both fundamental and applied research. Using 20 microsatellite loci, we investigated the composition of 53 schools (total n = 211) of adult and subadult migratory brook charr (Salvelinus fontinalis) sampled from the known feeding areas of two populations inhabiting Mistassini Lake (Québec, Canada). We specifically tested whether (i) school members originated from the same population, (ii) individuals from the same population within schools were kin (half- or full-siblings), and (iii) kin schooling relationships differed between sexes. Randomization tests revealed a tendency for most schools to be population specific, although some schools were population mixtures. Significantly more kin were found within schools than expected at random for both populations (approximately 21-34% of the total number of school members). This result, combined with the observed size range of individuals, indicated that stable associations between kin may occur beyond juvenile stages for up to 4 years. Nevertheless, a high proportion of school members were non-kin (approximately 66-79%). No differences were detected between sexes in the propensity to school with kin. We discuss the hypothesis that the stable kin groups, rather than arising from kin selection, may instead be a by-product of familiarity based on individual selection for the maintenance of local adaptations related to migration (natal and feeding area philopatry). Our results are noteworthy because they suggest that there is some degree of permanence in the composition of wild fish schools. Additionally, they support the hypothesis that schools can be hierarchically structured (from population members down to family groups) and are thus nonrandom genetic entities.     

Intergroup Aggression in Chimpanzees and War in Nomadic Hunter-Gatherers

Chimpanzee and hunter-gatherer intergroup aggression differ in important ways, including humans having the ability to form peaceful relationships and alliances among groups. This paper nevertheless evaluates the hypothesis that intergroup aggression evolved according to the same functional principles in the two species—selection favoring a tendency to kill members of neighboring groups when killing could be carried out safely. According to this idea chimpanzees and humans are equally risk-averse when fighting. When self-sacrificial war practices are found in humans, therefore, they result from cultural systems of reward, punishment, and coercion rather than evolved adaptations to greater risk-taking. To test this “chimpanzee model,” we review intergroup fighting in chimpanzees and nomadic hunter-gatherers living with other nomadic hunter-gatherers as neighbors. Whether humans have evolved specific psychological adaptations for war is unknown, but current evidence suggests that the chimpanzee model is an appropriate starting point for analyzing the biological and cultural evolution of warfare.     

A test of the randomness of paternity of members of maternal sibships in six captive groups of rhesus monkeys (Macaca mulatta)

Results of previous studies have shown that in captive groups of rhesus monkeys (Macaca mulatto)fathers associate more frequently with their own offspring than with those of other males and that mothers are most permissive of physical contact between their own infant and a juvenile when that juvenile shares the same father with her infant. These two observations suggest that the identity of offspring born in captive groups of rhesus monkeys is recognized by at least some adult members of the group. Consistent patterns of mating among mating seasons might explain this apparent recognition of offsprings’ paternity. Fathers, for example, might regularly associate with young who maintain a close relationship with females with whom they have previously mated, and mothers might selectively permit juveniles who maintain a close relationship with males with whom they have previously mated to associate with their infants. This hypothesis is tested in this paper by comparing the observed distribution of 70 maternal sibships, members of which were fathered by the same or by different adult males over a 4-year period in six captive groups of rhesus monkeys, with that distribution expected based on random mating from season to season. Seasonal mating patterns were found to be random. Preparations are now underway to test this hypothesis in several free-ranging groups.     

Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles

Molecular surveys in planktonic marine systems have unveiled a large novel diversity of small protists. A large part of this diversity belongs to basal heterotrophic stramenopiles and is distributed in a set of polyphyletic ribogroups (described from rDNA sequences) collectively named as MAST (MArine STramenopiles). In the few groups investigated, MAST cells are globally distributed and abundant bacterial grazers, therefore having a putatively large impact on marine ecosystem functioning. The main aim of this study is to reevaluate the MAST ribogroups described so far and to determine whether additional groups can be found. For this purpose, we used traditional and state-of-the-art molecular tools, combining 18S rDNA sequences from publicly available clone libraries, single amplified genomes (SAGs) of planktonic protists, and a pyrosequencing survey from coastal waters and sediments. Our analysis indicated a final set of 18 MAST groups plus 5 new ribogroups within Ochrophyta (named as MOCH). The MAST ribogroups were then analyzed in more detail. Seven were typical of anoxic systems and one of oxic sediments. The rest were clearly members of oxic marine picoplankton. We characterized the genetic diversity within each MAST group and defined subclades for the more diverse (46 subclades in 8 groups). The analyses of sequences within subclades revealed further ecological specializations. Our data provide a renovated framework for phylogenetic classification of the numerous MAST ribogroups and support the notion of a tight link between phylogeny and ecological distribution. These diverse and largely uncultured protists are widespread and ecologically relevant members of marine microbial assemblages.     

Tool‐like behavior in the sixbar wrasse,Thalassoma hardwicke (Bennett, 1830)

There are only a few documented cases of the use of either tools or substrates (anvils) as pseudotools in fishes. Described here is an anvil behavior of a labrid fish, Thalassoma hardwicke, observed under aquarium conditions. This fish was fed with pellets that are too large to swallow and too hard to break up into manageable bits using jaws only. The observed individual carried a pellet to an anvil to break it up into pieces small enough to be swallowed. This feeding behavior was frequently repeated (observed in detail about 15 times), nearly always successful, and remarkably consistent, suggesting that the rock selected for an anvil is remembered and its functional qualities or other factors may play a part in its choice. These observations agree with evidence for other advanced cognitive abilities in members of the genus Thalassoma and suggest that, for welfare demand, rocks with rough surfaces should be provided to these fish, especially when they receive hard food for variety. Zoo Biol 29:767–773, 2010. © 2010 Wiley‐Liss, Inc.     

GroupRank: Rank Candidate Genes in PPI Network by Differentially Expressed Gene Groups

Many cell activities are organized as a network, and genes are clustered into co-expressed groups if they have the same or closely related biological function or they are co-regulated. In this study, based on an assumption that a strong candidate disease gene is more likely close to gene groups in which all members coordinately differentially express than individual genes with differential expression, we developed a novel disease gene prioritization method GroupRank by integrating gene co-expression and differential expression information generated from microarray data as well as PPI network. A candidate gene is ranked high using GroupRank if it is differentially expressed in disease and control or is close to differentially co-expressed groups in PPI network. We tested our method on data sets of lung, kidney, leukemia and breast cancer. The results revealed GroupRank could efficiently prioritize disease genes with significantly improved AUC value in comparison to the previous method with no consideration of co-exprssed gene groups in PPI network. Moreover, the functional analyses of the major contributing gene group in gene prioritization of kidney cancer verified that our algorithm GroupRank not only ranks disease genes efficiently but also could help us identify and understand possible mechanisms in important physiological and pathological processes of disease.