Distribution, diversity and ecology of aerobic CO-oxidizing bacteria

Numerous studies indicate that carbon monoxide (CO) participates in a broader range of processes than any other single molecule, ranging from subcellular to planetary scales. Despite its toxicity to many organisms, a diverse group of bacteria that span multiple phylogenetic lineages metabolize CO. These bacteria are globally distributed and include pathogens, plant symbionts and biogeochemically important lineages in soils and the oceans. New molecular and isolation techniques, as well as genome sequencing, have greatly expanded our knowledge of the diversity of CO oxidizers. Here, we present a newly emerging picture of the distribution, diversity and ecology of aerobic CO-oxidizing bacteria.     

Portal protein diversity and phage ecology

Oceanic phages are critical components of the global ecosystem, where they play a role in microbial mortality and evolution. Our understanding of phage diversity is greatly limited by the lack of useful genetic diversity measures. Previous studies, focusing on myophages that infect the marine cyanobacterium Synechococcus, have used the coliphage T4 portal-protein-encoding homologue, gene 20 (g20), as a diversity marker. These studies revealed 10 sequence clusters, 9 oceanic and 1 freshwater, where only 3 contained cultured representatives. We sequenced g20 from 38 marine myophages isolated using a diversity of Synechococcus and Prochlorococcus hosts to see if any would fall into the clusters that lacked cultured representatives. On the contrary, all fell into the three clusters that already contained sequences from cultured phages. Further, there was no obvious relationship between host of isolation, or host range, and g20 sequence similarity. We next expanded our analyses to all available g20 sequences (769 sequences), which include PCR amplicons from wild uncultured phages, non-PCR amplified sequences identified in the Global Ocean Survey (GOS) metagenomic database, as well as sequences from cultured phages, to evaluate the relationship between g20 sequence clusters and habitat features from which the phage sequences were isolated. Even in this meta-data set, very few sequences fell into the sequence clusters without cultured representatives, suggesting that the latter are very rare, or sequencing artefacts. In contrast, sequences most similar to the culture-containing clusters, the freshwater cluster and two novel clusters, were more highly represented, with one particular culture-containing cluster representing the dominant g20 genotype in the unamplified GOS sequence data. Finally, while some g20 sequences were non-randomly distributed with respect to habitat, there were always numerous exceptions to general patterns, indicating that phage portal proteins are not good predictors of a phage's host or the habitat in which a particular phage may thrive.     

Endophyte microbiome diversity in micropropagated Atriplex canescens and Atriplex torreyi var griffithsii

Microbial diversity associated with micropropagated Atriplex species was assessed using microscopy, isolate culturing, and sequencing. Light, electron, and confocal microscopy revealed microbial cells in aseptically regenerated leaves and roots. Clone libraries and tag-encoded FLX amplicon pyrosequencing (TEFAP) analysis amplified sequences from callus homologous to diverse fungal and bacterial taxa. Culturing isolated some seed borne endophyte taxa which could be readily propagated apart from the host. Microbial cells were observed within biofilm-like residues associated with plant cell surfaces and intercellular spaces. Various universal primers amplified both plant and microbial sequences, with different primers revealing different patterns of fungal diversity. Bacterial and fungal TEFAP followed by alignment with sequences from curated databases revealed 7 bacterial and 17 ascomycete taxa in A. canescens, and 5 bacterial taxa in A. torreyi. Additional diversity was observed among isolates and clone libraries. Micropropagated Atriplex retains a complex, intimately associated microbiome which includes diverse strains well poised to interact in manners that influence host physiology. Microbiome analysis was facilitated by high throughput sequencing methods, but primer biases continue to limit recovery of diverse sequences from even moderately complex communities.     

On biomass diversity in ecology

We postulate that the biomass distribution function for an ecological population may be derived from the condition that the biomas diversity functional is maximal subject to an energetic constraint on the total biomass. This leads to a biomass distribution of the form \(p(m) = \bar m^{ - 1} \exp ( - m/\bar m)\) , where \(\bar m\) is the mean biomass per individual. The same condition yields a unique value for the biomass diversity functional. These predictions are tested against fishery data and found to be in good agreement. It is argued that the existence of a unique value for biomass diversity may provide a preliminary theoretical foundation for the observed upper limit to species diversity.     

Latitude,tree species diversity and the metabolic theory of ecology

The latitudinal diversity gradient (LDG) has been known for over a century, but its origin remains poorly understood. Because both latitude and species richness are broadly related to temperature, environmental temperature has been proposed as a driver of the LDG. Recently, Wang et al. (2009, Proceedings of the National Academy of Sciences USA, 106 ,13388–13392) used datasets compiled from tree distributions in eastern Asia and North America to compare the species richness?temperature relationship between the two regions at several spatial scales and framed their analyses in the context of the metabolic theory of ecology. Here, we show that their datasets lack comparability between eastern Asia and North America and that some aspects of their analyses probably biased their results, casting doubt on some of their conclusions.     

Phylogenetic diversity and ecology of environmental Archaea

On the basis of culture studies, Archaea were thought to be synonymous with extreme environments. However, the large numbers of environmental rRNA gene sequences currently flooding into databases such as GenBank show that these organisms are present in almost all environments examined to date. Large sequence databases and new fast phylogenetic software allow more precise determination of the archaeal phylogenetic tree, but also indicate that our knowledge of archaeal diversity is incomplete. Although it is apparent that Archaea can be found in all environments, the chemistry of their ecological context is mostly unknown.     

The ecology, genetic diversity, and phylogeny of Huaiyangshan virus in China

Surveys were carried out to better understand the tick vector ecology and genetic diversity of Huaiyangshan virus (HYSV) in both regions of endemicity and regions of nonendemicity. Haemaphysalis longicornis ticks were dominant in regions of endemicity, while Rhipicephalus microplus is more abundant in regions of nonendemicity. HYSV RNA was found in human and both tick species, with greater prevalence in H. longicornis and lesser prevalence in R. microplus. Phylogenetic analyses indicate that HYSV is a novel species of the genus Phlebovirus.     

Comment on biomass diversity in ecology

It is observed that a dynamical continuity equation for biomass distribution yields the asymptotic steady-state exponential dependencen=A exp( ) exhibited by certain fishery data, wherem is the biomass of an individual,n is the number of individuals per unit biomass interval, andA, are positive constants. This dynamical approach to biomass distribution is an alternative to the global maximization principle proposed recently by Lurié and Wagensberg.     

The diversity, distribution and ecology of diatoms from Antarctic inland waters

Diatoms are abundant and diverse in many Antarctic freshwaters, with a general trend of decreasing diversity moving southwards. They form an important component of many benthic algal communities in streams and standing waters but are generally less common in the phytoplankton. Diatoms are excellent ecological indicator species and, because their remains are preserved in many sedimentary environments, there appears to be a great potential for palaeoenvironmental reconstruction and the examination of past diversity. A lack of taxonomic precision and consistency, coupled with the insufficient collection from some geographical areas, makes the estimation of the number of Antarctic diatom species problematic.     

Rhizobia from wild legumes: diversity, taxonomy, ecology, nitrogen fixation and biotechnology

Wild legumes (herb or tree) are widely distributed in arid regions and actively contribute to soil fertility in these environments. The N2-fixing activity and tolerance to drastic conditions may be higher in wild legumes than in crop legumes. The wild legumes in arid zones harbor diverse and promiscuous rhizobia in their root-nodules. Specificity existed only in few rhizobia from wild legumes, however, the majority of them are with wide host range. Based on phenotypic characteristics and molecular techniques (protein profiles, polysaccharides, plasmids, DNA-DNA hybridization, 16SrRNA, etc.), the root-nodule bacteria that was isolated from wild legumes had been classified into four genera (Rhizobium, Bradyrhizobium, Mesorhizobium and Sinorhizobium). The rhizobia of wild legumes in arid zones, exhibit higher tolerance to the prevailing adverse conditions, e.g. salt stress, elevated temperatures and desiccation. These rhizobia may be used to inoculate wild, as well as, crop legumes, cultivated in reclaimed desert lands. Recent reports indicated that the wild-legume rhizobia formed successful symbioses with some grain legumes. Moreover, intercropping of some N2-fixing tree legumes (e.g. Lablab, Leucaena, Sesbania, etc.) to pasture grasses improved biomass yield and herb quality. In recent years, the rhizobia of wild legumes turn the attention of biotechnologists. These bacteria may have specific traits that can be transferred to other rhizobia through genetic engineering tools or used to produce industrially important compounds. Therefore, these bacteria are very important from both economic and environmental points of view.     

生态学的多样性指数:功能与系统发育

生物多样性是生态学的核心问题。传统的多样性指数仅包含物种数和相对多度的信息,这类基于分类学的多样性指数并不能很好地帮助理解群落构建和生态系统功能。不同物种对群落构建和生态系统功能所起到的作用类型和贡献也不完全相同,且物种在生态过程中的作用和贡献往往与性状密切相关,因此功能多样性已经成为反映物种群落构建、干扰以及环境因素对群落影响的重要指标。同时,由于亲缘关系相近的物种往往具有相似的性状,系统发育多样性也可以作为功能多样性的一个替代。功能多样性和系统发育多样性各自具有优缺点,但二者均比分类多样性更能揭示群落和生态系统的构建、维持与功能。     

Physical variability,diversity gradients and the ecology of temperate and tropical reefs

Traditionally, compared with the tropics, temperate systems are believed to: (i) have environments which are less favourable (i.e. harsher, more variable and less predictable); and (ii) support communities which are less diverse. Explanations for differences between temperate and tropical communities, including differences in diversity, generally rely on the former notion. The evidence for these ideas is, at best, equivocal. Organisms are subjected to physical stresses and disturbances on both temperate and tropical reefs. Communities on temperate reefs are not invariably less diverse than those in the tropics, at least at small spatial scales. Finally, there is as yet little evidence of genuine differences between the ecology of temperate and tropical communities. There is, however, much small-scale, spatial patchiness in the structure of reef communities and their physical environment. This patchiness in structure may result from patchiness in biological factors (e.g. recruitment) or in the physical environment. This small-scale variation in environmental factors may prove to be a more important determinant of community structure than the large-scale, latitudinal trends some ecologists have been obsessed with.     

Introduction. Antarctic ecology: from genes to ecosystems. Part 2. Evolution, diversity and functional ecology

The Antarctic biota has evolved over the last 100 million years in increasingly isolated and cold conditions. As a result, Antarctic species, from micro-organisms to vertebrates, have adapted to life at extremely low temperatures, including changes in the genome, physiology and ecological traits such as life history. Coupled with cycles of glaciation that have promoted speciation in the Antarctic, this has led to a unique biota in terms of biogeography, patterns of species distribution and endemism. Specialization in the Antarctic biota has led to trade-offs in many ecologically important functions and Antarctic species may have a limited capacity to adapt to present climate change. These include the direct effects of changes in environmental parameters and indirect effects of increased competition and predation resulting from altered life histories of Antarctic species and the impacts of invasive species. Ultimately, climate change may alter the responses of Antarctic ecosystems to harvesting from humans. The unique adaptations of Antarctic species mean that they provide unique models of molecular evolution in natural populations. The simplicity of Antarctic communities, especially from terrestrial systems, makes them ideal to investigate the ecological implications of climate change, which are difficult to identify in more complex systems.     

Ants that associate with Lycaeninae butterfly larvae: diversity, ecology and biogeography

Abstract. Field data on associations of butterfly larvae with ants were collated for 435 species of the subfamily Lycaeninae to analyse patterns in the identity, diversity and ecology of attendant ants. Worldwide, members of at least fifty-three ant genera from six subfamilies associate with Lycaeninae larvae. All these ant genera also forage for other liquid carbohydrate food sources. Species of Crematogaster and Camponotus constitute by far the most important ant associates of Lycaeninae larvae. Diversity of butterfly–ant associations, as measured by Hurlbert rarefaction, is highest in the Oriental, Australian and Nearctic faunal regions, and lower in Africa and the Palaearctic. The Neotropical region could not be assessed separately due to paucity of data. Multiple regression analyses revealed that the number of Lycaeninae species associated with a particular ant genus in a facultatively mutualistic manner is largely determined by the ecological prevalence and geographical distribution, but does not correlate with species richness, of an ant genus. This opportunism is suggested to be the key variable supporting the geographically and taxonomically widespread occurrence of ant–caterpillar mutualism in the Lycaeninae. Obligate interactions are much more specific and almost exclusively involve ecologically dominant ants with long-lived colonies. Neither species richness nor geographical distribution of an ant genus are significant predictors. In such associations, the role of ants shifts from visitors to hosts, and patterns of host use and specificity resemble those known from inquiline ant guests.     

Gap ecology in Florida scrub: Species occurrence,diversity and gap properties

Questions: Studies of gap effects have been conducted mainly in forests. We studied gap ecology in a pyrogenic Ceratiola ericoides (Florida rosemary) dominated shrubland and asked: How do gap size and the frequency of large gaps change across the fire chronosequence? Do larger gaps differ from smaller gaps in vegetation structure or species diversity? Are effects of gaps independent of, or dependent upon, time‐since‐fire? Are larger gaps refugia for herbs and subshrubs? Location: Archbold Biological Station, Lake Wales Ridge, south‐central Florida, USA. Methods: We investigated plant species occurrence and diversity in 805 gaps (areas free of shrubs taller than 50 cm) in 28 fire‐dependent Florida rosemary scrub sites. We collected quantitative cover data in a subset of seven sites. Results: Gap area distribution was lognormal. The largest gaps occurred throughout all but the longest time‐since‐fire intervals. Gaps were smallest in the longest unburned site but otherwise did not show strong patterns across the fire chronosequence. Species diversity measures increased with increasing gap area, with herbaceous diversity increasing with both gap area and bare sand. Herb diversity (H') decreased with time‐since‐fire. Larger gaps are refugia for some species. Of 14 species occurring in 25–75% of gaps, 13 had increased occupancy with increasing gap area, and gap area was the strongest predictor of occupancy for seven species of herbs and shrubs. Time‐since‐fire was the strongest predictor of occupancy for five species, including four ground lichens that increased with time‐since‐fire. Conclusions: Community structure within Florida scrub gaps is influenced by gap size, which in turn is affected by fire, the dominant ecological disturbance. We present a conceptual model that considers both gap size and time‐since‐fire as drivers of community structure and herbaceous plant diversity in Florida scrub. Because gap properties (independently of fire) have strong influences on species assemblages in Florida rosemary scrub gaps, fire management should consider the number and size of gaps across the landscape.