The diversity of temporal niches in mammals

The division of animals into those that are diurnal (day-active) and those that are nocturnal (night-active) is widely recognized. However, closer examination of the selection of temporal niches by mammalian species reveals the existence of a gradient of diurnality between and within species, wherein “diurnal” and “nocturnal” are merely the opposite ends of a continuum. Evidence against a simple diurnal - nocturnal dichotomy includes the existence of species without any preference for time of day, species with a crepuscular pattern of activity, species containing both diurnal and nocturnal individuals, species containing individuals that spontaneously shift from a nocturnal to a diurnal activity pattern, species showing degrees of diurnality greater or smaller than those of other species, organismal variables exhibiting degrees of diurnality greater or smaller than those of other variables, and species having different temporal patterns under the effects of different environmental variables. Research on the neural processes responsible for temporal niche selection has revealed no fundamental difference between the circadian clocks of diurnal and nocturnal animals, but recent findings suggest that different output pathways from the clock in a given species may operate with different circadian phases, thus providing an explanation for why different body functions in the same individual are subjected to different temporal niche selections.     

Microbial diversity of soda lakes

Soda lakes are highly alkaline extreme environments that form in closed drainage basins exposed to high evaporation rates. Because of the scarcity of Mg²⁺ and Ca²⁺ in the water chemistry, the lakes become enriched in CO₃ ²⁻ and Cl⁻, with pHs in the range 8 to >12. Although there is a clear difference in prokaryotic communities between the hypersaline lakes where NaCl concentrations are >15% w/v and more dilute waters, i.e., NaCl concentrations about 5% w/v, photosynthetic primary production appears to be the basis of all nutrient recycling. In both the aerobic and anaerobic microbial communities the major trophic groups responsible for cycling of carbon and sulfur have in general been identified. Systematic studies have shown that the microbes are alkaliphilic and many represent separate lineages within accepted taxa, while others show no strong relationship to known prokaryotes. Although alkaliphiles are widespread it seems probable that these organisms, especially those unique to the hypersaline lakes, evolved separately within an alkaline environment. Although present-day soda lakes are geologically quite recent, they have probably existed since archaean times, permitting the evolution of independent communities of alkaliphiles since an early period in the Earth's history. Received: January 22, 1998 / Accepted: February 16, 1998     

Microbial diversity and biogeochemical cycling in soda lakes

Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art ‘meta-omic’ techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments.     

Size diversity and species diversity relationships in fish assemblages of Western Palearctic lakes

Body size, coupled with abundance and taxonomy, may help to understand the mechanisms shaping community structure. Since the body size of fish is closely related to their trophic niche, size diversity (based on individual body size) of fish communities may capture intraspecific variations in fish trophic niches that are not detected by species diversity. Thus, the relationship between size diversity and species diversity may help to integrate variation at both intraspecific and interspecific levels. We studied the relationship between species diversity and size diversity as a measure of the degree of overlap in size among species and thereby the potential overlap in niches in a community. We hypothesized that the relationship between size diversity and species would be different across the European continent due to different levels of size overlap in fish communities. The data were derived from samplings of fish communities using standardised benthic gill nets in 363 lakes. At the continental scale, size diversity increased with species diversity; at the ecoregion scale, the slope of the relation changed across the continent, with the greatest mismatch occurring in northern Europe where communities comprised only one or a few species, but each of which exhibited a great range in size. There was an increase in slope towards the south with significant relations for four out of six ecoregions. The steeper size diversity‐species diversity slope at lower latitudes is attributable to a lower overlap in fish size and thus likely to finer niche separation. Our results also suggest that size diversity is not a strong surrogate for species diversity in European lake fish communities. Thus, particularly in fish communities composed of few species, measuring size diversity may help to detect potential functional variation which may be neglected by measuring species diversity alone.     

ospC diversity in Borrelia burgdorferi: different hosts are different niches

The outer surface protein C (ospC) locus of the Lyme disease bacterium, Borrelia burgdorferi, is at least an order of magnitude more variable than other genes in the species. This variation is classified into 22 ospC major groups, 15 of which are found in the northeastern United States. The frequency distributions of ospC within populations suggest that this locus is under balancing selection. In multiple-niche polymorphism, a type of balancing selection, diversity within a population can be maintained when the environment is heterogeneous and no one genotype has the highest fitness in all environments. Genetically different individuals within vertebrate species and different vertebrate species constitute diverse environments for B. burgdorferi. We examined four important host species of B. burgdorferi and found that the strains that infected each species had different sets of ospC major groups. We found no variation among conspecific hosts in the ospC major groups of their infecting strains. These results suggest multiple niches create balancing selection at the ospC locus.     

Genetic diversity of cyanobacteria in four eutrophic lakes

Recent studies indicate genetic diversity of cyanobacteria in eutrophic lakes is not represented well by culture collections or morphology. Yet, few studies have investigated genetic richness and evenness of cyanobacteria using culture-independent methods. We compared the genetic structure of cyanobacteria supported by four neighboring eutrophic lakes during the ice-free season. The partial phycobilincpcB/A genes plus intergenic spacer (PC-IGS) was used as a genetic marker.Sequences were phylogeneticallygrouped by maximum likelihood into genotypes representing sub-genera of the major taxa. Genotypes fell into genera commonly observed by microscopy in these lakes including Microcystis, Aphanizomenon, Chroococcus, Anabaena, and Cylindrospermopsis. Only three genotypes were shared among all four lakes, despite significant water flowage between lakes.A Parsimony P-test indicated lakes were significantly (p=0.01) clustered on the maximum likelihood tree. Pairwise differences using Unifrac distance were moderately or not significant. Analysis of molecular variance (AMOVA) indicated genetic variation among all genotypes (φ=0.06, p<0.001) and 94% of variability occurred within lakes rather than between lakes (6%), explaining the lack of pairwise differences between lakes. Lorenze curves of genotype abundance in each lake showed genetic structure was only moderately uneven (Gini coefficients of 0.37-0.5) indicating lakes did not support dominant genotypes. Overall, results from this study suggest diversity of cyanobacteria is shaped by heterogeneity within lakes (temporally or spatially) and relatively even population structures.     

Environmental factors shaping the ecological niches of ammonia-oxidizing archaea

For more than 100 years it was believed that bacteria were the only group responsible for the oxidation of ammonia. However, recently, a new strain of archaea bearing a putative ammonia monooxygenase subunit A ( amoA ) gene and able to oxidize ammonia was isolated from a marine aquarium tank. Ammonia-oxidizing archaea (AOA) were subsequently discovered in many ecosystems of varied characteristics and even found as the predominant causal organisms in some environments. Here, we summarize the current knowledge on the environmental conditions related to the presence of AOA and discuss the possible site-related properties. Considering these data, we deduct the possible niches of AOA based on pH, sulfide and phosphate levels. It is proposed that the AOA might be important actors within the nitrogen cycle in low-nutrient, low-pH, and sulfide-containing environments.     

Phylogenetic diversity,trait diversity and niches: species assembly of ferns along a tropical elevational gradient

Aim To analyse the structure of pteridophyte assemblages, based on phylogenetic relatedness and trait properties, along an elevational gradient. Ecological theory predicts that co‐occurring species may be: randomly selected from a regional pool; ecologically sorted so that they are functionally different hence resulting in reduced competition (overdispersion); or functionally similar as an adaptation to specific ecological conditions (clustering). Location Braulio Carrillo National Park and Cerro de la Muerte, Costa Rica, Central America. Methods We used an empirical dataset of the quantitative pattern of species occurrences and individual numbers of ferns within 156 plots along a tropical elevational gradient to test whether directed ecological sorting might cause deviations in patterns of trait and phylogenetic diversity. Mean pairwise distances of species based on phylogenetic and trait properties were compared with two different sets of null assemblages, one maintaining species frequency distributions (constrained) and one not (unconstrained). Results Applying different null models resulted in varying degrees of overdispersion and clustering, but overall patterns of deviation from random expectations remained the same. Contrary to theoretical predictions, phylogenetic and trait diversity were relatively independent from one another. Phylogenetic diversity showed no patterns along the elevational gradient, whereas trait diversity showed significant trends for epiphytes. Main conclusions Under stressful environmental conditions (drought at low elevations and frost at high elevations), epiphytic fern assemblages tended to be clustered with respect to trait characteristics, which suggests environmental filtering. Conversely, under less extreme environmental conditions (middle of the transect), the sorting was biased towards high differentiation (overdispersion), presumably because of interspecific competition and trait shifts among closely related species (character displacement).     

巴丹吉林沙漠盐湖微生物多样性

【目的】研究内蒙古巴丹吉林沙漠碱性盐湖中的原核生物多样性及其与环境因子之间的关系。【方法】利用分子生物学方法构建16S rRNA基因克隆文库,对盐湖中的嗜盐碱微生物进行系统发育分析;利用R语言绘图,对不同盐湖的微生物群落结构进行对比研究。【结果】该区域盐湖含盐量很高,矿化度达165g/L-397 g/L。同时,水体呈强碱性,p H均在10以上。三个湖的盐度和p H值等理化参数有梯度变化,因此微生物多样性和群落结构存在明显差异。整体而言,细菌的多样性大于古菌。样品中含有的主要的细菌门类为γ-变形菌亚门(Gammaproteobacteria)、拟杆菌门(Bacteroidetes)、α-变形菌亚门(Alphaproteobacteria)、厚壁菌门(Firmicutes)、疣微菌门(Verrucomicrobia),古菌则全部属于广古菌门(Euryarchaeota)中的盐杆菌科(Halobacteriaceae)。【结论】盐度是决定细菌群落结构的主要因素,古菌群落结构则由多种环境因素综合影响。一些已知的嗜盐碱菌,如Roseinatronobacter spp.、Halohasta spp.等,可以生活在比其盐度和碱度生长范围更高的极端盐碱环境中。此外,样品中还含有大量未培养的嗜盐碱细菌和古菌,对进一步开发极端盐碱环境中的微生物资源有重要意义。     

Environmental gradients and the horizontal distribution of microcrustaceans in lakes

1. The assemblage of suspension‐feeding microcrustaceans in lakes changes along a habitat gradient from nearshore to offshore. This gradient of microcrustaceans was explored in relation to differences in macrophytes and the associated changes in water chemistry, food resources and types of predators.
2. Some microcrustacean species were littoral or limnetic specialists, while others changed their distribution along this horizontal habitat gradient on a diel or seasonal basis. Distribution patterns were similar in a lake and a pond which differed in extent of macrophyte habitat.
3. There was a large shift in the composition of sestonic food, indicating heterotrophic seston nearshore and more autotrophic seston offshore. Sit‐and‐wait predators of microcrustaceans (e.g. Enallagma spp.) dominated nearshore and cruising predators (e.g. Leptodora kindtii Focke) were more common offshore.
4. A reciprocal transplant experiment revealed that littoral specialists could survive equally well when fed littoral or limnetic seston, while limnetic specialists performed poorly when fed littoral seston. Food resources may be important in determining where some microcrustacean species live along this horizontal habitat gradient.     

Activity and diversity of haloalkaliphilic methanogens in Central Asian soda lakes

Methanogens are of biotechnological interest because of their importance in biogas production. Here we investigate the suitability of sediments from Central Asian soda lakes as inoculum for high pH methane-producing bioreactors. Methane production in these sediments was modest (up to 2.5 μmol mL sediment), with methanol and hydrogen as the preferred substrates. The responsible methanogenic community was characterized based on mcrA gene sequences. McrA gene sequences so far specific to these habitats indicated the presence of two clusters within the orders Methanobacteriales and Methanomicrobiales, one apparently including representatives of the genus Methanocalculus and another distantly related to the genus Methanobacterium.     

Environmental heterogeneity among lakes promotes hyper β‐diversity across phytoplankton communities

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Environmental predictors of electroactive bacterioplankton in small boreal lakes

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