Community phylogenetic analysis of moderately thermophilic cyanobacterial mats from China, the Philippines and Thailand

Most community molecular studies of thermophilic cyanobacterial mats to date have focused on Synechococcus occurring at temperatures of ~50–65°C. These reveal that molecular diversity exceeds that indicated by morphology, and that phylogeographic lineages exist. The moderately thermophilic and generally filamentous cyanobacterial mat communities occurring at lower temperatures have not previously been investigated at the community molecular level. Here we report community diversity in mats of 42–53°C recovered from previously unstudied geothermal locations. Separation of 16S rRNA gene-defined genotypes from community DNA was achieved by DGGE. Genotypic diversity was greater than morphotype diversity in all mats sampled, although genotypes generally corresponded to observed morphotypes. Thirty-six sequences were recovered from DGGE bands. Phylogenetic analyses revealed these to form novel thermophilic lineages distinct from their mesophilic counterparts, within Calothrix, Cyanothece, Fischerella, Phormidium, Pleurocapsa, Oscillatoria and Synechococcus. Where filamentous cyanobacterial sequences belonging to the same genus were recovered from the same site, these were generally closely affiliated. Location-specific sequences were observed for some genotypes recovered from geochemically similar yet spatially separated sites, thus providing evidence for phylogeographic lineages that evolve in isolation. Other genotypes were more closely affiliated to geographically remote counterparts from similar habitats suggesting that adaptation to certain niches is also important.     

Isotopic niches do not follow the expectations of niche conservatism in the bird genus Cinclodes

Phenotypic traits are expected to be more similar among closely related species than among species that diverged long ago (all else being equal). This pattern, known as phylogenetic niche conservatism, also applies to traits that are important to determine the niche of species. To test this hypothesis on ecological niches, we analysed isotopic data from 254 museum study skins from 12 of the 16 species of the bird genus Cinclodes and measured stable isotope ratios for four different elements: carbon, nitrogen, hydrogen and oxygen. We find that all traits, measured individually, or as a composite measurement, lack any phylogenetic signal, which in turn suggests a high level of lability in ecological niches. We compared these metrics to the measurements of morphological traits in the same genus and found that isotopic niches are uniquely evolutionarily labile compared to other traits. Our results suggest that, in Cinclodes, the realized niche evolves much faster than expected by the constraints of phylogenetic history and poses the question of whether this is a general pattern across the tree of life     

Enzymo-Serological Comparison of Proteolytic Enzymes Produced by Salmonella Species and Other Enterobacteria

The proteolytic enzymes produced by 11 Salmonella species of the Sub-genera I, II and IV, have been compared by a so-called enzymo-serological procedure. In sub-genus I, the enzymes of S. schleissheim and S. abortus-bovis showed an identical, or closely related, serological picture, whereas S. texas was serologically distinct. All the 7 examined strains of sub-genus II produced proteolytic enzymes which were serologically very similar, or identical. No enzymo-serological cross-reactions were observed between these organisms and the members of sub-genus I. The only examined species of sub-genus IV, S. argentina, was enzymo-serologically distinct from all other species. Intergeneric cross-reactions occurred between the enzymes from Salmonella species, Enterobacter (Aerobacter) cloacae and Serratia marcescens. The significance of these cross-reactions is discussed.     

Species assortment or habitat filtering: a case study of spider communities on lake islands

Competition theory predicts that species of similar ecological niches are less likely to coexist than species with different niches, a process called species assortment. In contrast, the concept of habitat filtering implies that species with similar ecological requirements should co-occur more often than expected by chance. Here we use environmental and ecological data to assess patterns of co-occurrence of regional communities of spiders distributed across two assemblies of lake islands in northern Poland. We found aggregated and random co-occurrences of species of the same genus and a significant tendency of species segregation across genera. We also found that species of the same genus react similarly to important environmental variables. A comparison of ecological traits of species of the local communities with those expected from a random sample from the regional Polish species pool corroborated partly the habitat filtering hypothesis. On the other hand, we did not find evidence for species assortment. Our results also imply that at least some observed species co-occurrences result from niche differentiation.     

Effect of Temperature and Light on Growth of and Photosynthesis by Synechococcus Isolates Typical of Those Predominating in the Octopus Spring Microbial Mat Community of Yellowstone National Park

Previous molecular analysis of the Octopus Spring cyanobacterial mat revealed numerous genetically distinct 16S rRNA sequences from predominant Synechococcus populations distantly related to the readily cultivated unicellular cyanobacterium Synechococcus lividus. Patterns in genotype distribution relative to temperature and light conditions suggested that the organisms contributing these 16S rRNA sequences may fill distinct ecological niches. To test this hypothesis, Synechococcus isolates were cultivated using a dilution and filtration approach and then shown to be genetically relevant to natural mat populations by comparisons of similarities of 16S rRNA genes and 16S-23S internal transcribed spacer (ITS) regions. Most isolates were identical or nearly identical at both loci to predominant mat genotypes; others showed 1- to 2-nucleotide differences at the 16S rRNA locus and even greater difference in ITS sequences. Isolates with predominant mat genotypes had distinct temperature ranges and optima for growth that were consistent with their distributions in the mat. Isolates with genotypes not previously detected or known to be predominant in the mat exhibited temperature ranges and optima that were not representative of predominant mat populations and also grew more slowly. Temperature effects on photosynthesis did not reflect temperature relations for growth. However, the isolate with the highest temperature optimum and upper limit was capable of performing photosynthesis at a higher temperature than other isolates. Growth rate and photosynthetic responses provided evidence for light acclimation but evidence of, at best, only subtle light adaptation.     

Temperature as an Ecological Resource

Ectothermic vertebrates respond to the temperature of theirhabitat in a manner that is remarkably similar to their responseto more traditional ecological resources such as food. We reviewthe response to temperature primarily from literature on fishesin terms of ecological concepts related to niche theory andcompetition. The width of the fundamental thermal niche is about4°C when measured by a mean plus and minus one standarddeviation of the distribution of temperature occupied in a laboratorygradient. Fish of temperate freshwater appear to fall into threethermal guilds along the temperature resource axis —cold,cool, and warm water fishes. Realized thermal niches are similarin central tendency to fundamental niches, but niche width appearsto be more narrow for the realized niche in limited sample data.The success of interference competition for space with preferredtemperature is tied to social dominance in a manner analogousto food competition. Thermal niche shifts in the face of interspecificcompetition for preferred temperature appear supported by onelaboratory study. Exploitation competition in respect to temperatureseems nebulous. If animals successfully compete for their thermalniche, growth and perhaps other measures of fitness are maximized.Cost/benefit models for thermal resources and food resourceslead to similar predictions about resource use. We suggest thatviewing temperature and other niche axes in the way ecologistshave viewed food resources would be useful.     

Beyond temperature coupling: Effects of temperature on ectotherm signaling and mate choice and the implications for communication in multispecies assemblages

Many organisms share communication channels, generating complex signaling environments that increase the risk of signal interference. Variation in abiotic conditions, such as temperature, may further exacerbate signal interference, particularly in ectotherms. We tested the effects of temperature on the pulse rate of male signals in a community of Oecanthus tree crickets, and for one focal species we also assessed its effect on female pulse rate preferences and motivation to seek mates. We confirm prior findings of temperature‐dependent signals that result in increasing signal similarity at lower temperatures. Temperature also affected several aspects of female preferences: The preferred pulse rate value was temperature dependent, and nearly perfectly coupled with signal pulse rate; the range of pulse rate values that females found attractive also increased with temperature. By contrast, the motivation of females to perform phonotaxis was unaffected by temperature. Thus, at lower temperatures the signals of closely related species were more similar and females more discriminating. However, because signal similarity increased more strongly than female discrimination, signal interference and the likelihood of mismating may increase as temperatures drop. We suggest that a community approach will be useful for understanding the role of environmental variability in the evolution of communication systems.     

The evolution of climate tolerance in conifer‐feeding aphids in relation to their host's climatic niche

Climate adaptation has major consequences in the evolution and ecology of all living organisms. Though phytophagous insects are an important component of Earth's biodiversity, there are few studies investigating the evolution of their climatic preferences. This lack of research is probably because their evolutionary ecology is thought to be primarily driven by their interactions with their host plants. Here, we use a robust phylogenetic framework and species‐level distribution data for the conifer‐feeding aphid genus Cinara to investigate the role of climatic adaptation in the diversity and distribution patterns of these host‐specialized insects. Insect climate niches were reconstructed at a macroevolutionary scale, highlighting that climate niche tolerance is evolutionarily labile, with closely related species exhibiting strong climatic disparities. This result may suggest repeated climate niche differentiation during the evolutionary diversification of Cinara. Alternatively, it may merely reflect the use of host plants that occur in disparate climatic zones, and thus, in reality the aphid species' fundamental climate niches may actually be similar but broad. Comparisons of the aphids' current climate niches with those of their hosts show that most Cinara species occupy the full range of the climatic tolerance exhibited by their set of host plants, corroborating the hypothesis that the observed disparity in Cinara species' climate niches can simply mirror that of their hosts. However, 29% of the studied species only occupy a subset of their hosts' climatic zone, suggesting that some aphid species do indeed have their own climatic limitations. Our results suggest that in host‐specialized phytophagous insects, host associations cannot always adequately describe insect niches and abiotic factors must be taken into account.     

Deterministic processes dominate nematode community structure in the Fynbos Mediterranean heathland of South Africa

In many ecosystems, the factors that determine landscape-scale community structure of soil nematodes are poorly understood. We were interested in discovering whether deterministic or stochastic factors dominate nematode community variation. We used a novel metagenetic approach to investigate variation in nematode community structure in the Fynbos vegetation of South Africa. We compared 23 samples of soil nematode communities from five different Fynbos landscapes. Nematode DNA was 454-pyrosequenced for the 18S rRNA gene. We investigated the community structure, diversity, and the relative role of both deterministic (niche-based) and neutral processes may play in delimiting the nematode phylogenetic community structure in different Fynbos vegetation types. Nematode diversity showed no relationship to any measured soil parameter. The phylogenetic signal showed that more closely related types of nematodes in the Fynbos tended to co-occur more often than would be expected by chance, demonstrating that (a) closely related lineages occupy similar niches spatially and (b) community variation is influenced more by determinism than stochasticity. The standardised beta mean nearest taxon distance (ses.βMNTD) index showed no association with vegetation type. Both ses.NTI (nearest taxon index) and ses.βMNTD deviated significantly from null models, indicating that deterministic processes were important in the assembly of nematode communities. Furthermore, at local scale, the ses.NTI was significantly higher than null expectations, indicating that co-occurrence of related nematode lineages is determined by the differences in environmental conditions across the sites. We conclude that in the Fynbos there is niche overlap between closely related types of nematodes, that nematode speciation tends to occur conservatively into closely related niches, and that the phylogenetic community structure reveals that deterministic (rather than stochastic) processes are more important in delimiting the community assembly.     

Microheterogeneity in 16S Ribosomal DNA-Defined Bacterial Populations from a Stratified Planktonic Environment Is Related to Temporal Changes and to Ecological Adaptations

Temporal changes of the bacterioplankton from a meromictic lake (Lake Vilar, Banyoles, Spain) were analyzed with four culture-independent techniques: epifluorescence microscopy, PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting, fluorescence in situ whole-cell hybridization and flow cytometry sorting. Microscopically, blooms of one cyanobacterium (Synechococcus sp.-like), one green sulfur bacterium (Chlorobium phaeobacteroides-like), and one purple sulfur bacterium (Thiocystis minor-like) were observed at different depths and times. DGGE retrieved these populations and, additionally, populations related to the Cytophaga-Flavobacterium-Bacteroides phylum as predominant community members. The analyses of partial 16S ribosomal DNA sequences from the DGGE fingerprints (550 bp analyzed) revealed higher genetic diversity than expected from microscopic observation for most of these groups. Thus, the sequences of two Synechococcus spp. (both had a similarity of 97% to Synechococcus sp. strain PCC6307 in 16S rRNA), two Thiocystis spp. (similarities to Thiocystis minor of 93 and 94%, respectively), and three Cytophaga spp. (similarities to Cytophaga fermentans of 88 and 89% and to Cytophaga sp. of 93%, respectively) were obtained. The two populations of Synechococcus exhibited different pigment compositions and temporal distributions and their 16S rRNA sequences were 97.3% similar. The two Thiocystis populations differed neither in pigment composition nor in morphology, but their 16S rRNA sequences were only 92.3% similar and they also showed different distributions over time. Finally, two of the Cytophaga spp. showed 96.2% similarity between the 16S rRNA sequences, but one of them was found to be mostly attached to particles and only in winter. Thus, the identity of the main populations changed over time, but the function of the microbial guilds was maintained. Our data showed that temporal shifts in the identity of the predominant population is a new explanation for the environmental 16S rRNA microdiversity retrieved from microbial assemblages and support the hypothesis that clusters of closely related 16S rRNA environmental sequences may actually represent numerous closely related, yet ecologically distinct, populations.     

Complementary strengths of spatially-explicit and multi-species distribution models

Species distribution models (SDMs) project the outcome of community assembly processes – dispersal, the abiotic environment and biotic interactions – onto geographic space. Recent advances in SDMs account for these processes by simultaneously modeling the species that comprise a community in a multivariate statistical framework or by incorporating residual spatial autocorrelation in SDMs. However, the effects of combining both multivariate and spatially-explicit model structures on the ecological inferences and the predictive abilities of a model are largely unknown. We used data on eastern hemlock Tsuga canadensis and five additional co-occurring overstory tree species in 35 569 forest stands across Michigan, USA to evaluate how the choice of model structure, including spatial and non-spatial forms of univariate and multivariate models, affects ecological inference about the processes that shape community composition as well as model predictive ability. Incorporating residual spatial autocorrelation via spatial random effects did not improve out-of-sample prediction for the six tree species, although in-sample model fit was higher in the spatial models. Spatial models attributed less variation in occurrence probability to environmental covariates than the non-spatial models for all six tree species, and estimated higher (more positive) residual co-occurrence values for most species pairs. The non-spatial multivariate model was better suited for evaluating habitat suitability and hypotheses about the processes that shape community composition. Environmental correlations and residual correlations among species pairs were positively related, perhaps indicating that residual correlations were due to shared responses to unmeasured environmental covariates. This work highlights the importance of choosing a non-spatial model formulation to address research questions about the species–environment relationship or residual co-occurrence patterns, and a spatial model formulation when within-sample prediction accuracy is the main goal.     

Cyanobacterial Ecotypes in Different Optical Microenvironments of a 68°C Hot Spring Mat Community Revealed by 16S-23S rRNA Internal Transcribed Spacer Region Variation

We examined the population of unicellular cyanobacteria (Synechococcus) in the upper 3-mm vertical interval of a 68°C region of a microbial mat in a hot spring effluent channel (Yellowstone National Park, Wyoming). Fluorescence microscopy and microsensor measurements of O₂ and oxygenic photosynthesis demonstrated the existence of physiologically distinct Synechococcus populations at different depths along a light gradient quantified by scalar irradiance microprobes. Molecular methods were used to evaluate whether physiologically distinct populations could be correlated with genetically distinct populations over the vertical interval. We were unable to identify patterns in genetic variation in Synechococcus 16S rRNA sequences that correlate with different vertically distributed populations. However, patterns of variation at the internal transcribed spacer locus separating 16S and 23S rRNA genes suggested the existence of closely related but genetically distinct populations corresponding to different functional populations occurring at different depths.     

The influence of light and moisture gradients on the attack rate of parasitoids foraging for hosts in a laboratory arena (Hymenoptera: Pteromalidae)

Microhabitat preferences of four parasitoids (Hymenoptera: Pteromalidae) of house fly pupae were measured in a two-dimensional arena containing perpendicular light and moisture gradients. Parasitism by Muscidifurax raptorand Nasonia vitripenniswas greatest in dry substrates, with the latter preferring bright illumination and the former tending to prefer dark. Urolepis rufipesselected bright illumination and moist substrates, attacking the most hosts at bright-moist and dim-moist microhabitats. Spalangia cameroniexhibited no main-effect preference for light intensity or moisture, although parasitism was highest at dim-moist, dark-wet, and dark-moist microhabitats. These results demonstrate that simple abiotic attributes, such as light intensity and substrate moisture concentration, are important in defining some dimensions of the niches of these parasitoids.     

Multi-year dynamics of fine-scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic,bottom-up factors

Currently defined ecotypes in marine cyanobacteria Prochlorococcus and Synechococcus likely contain subpopulations that themselves are ecologically distinct. We developed and applied high-throughput sequencing for the 16S-23S rRNA internally transcribed spacer (ITS) to examine ecotype and fine-scale genotypic community dynamics for monthly surface water samples spanning 5 years at the San Pedro Ocean Time-series site. Ecotype-level structure displayed regular seasonal patterns including succession, consistent with strong forcing by seasonally varying abiotic parameters (e.g. temperature, nutrients, light). We identified tens to thousands of amplicon sequence variants (ASVs) within ecotypes, many of which exhibited distinct patterns over time, suggesting ecologically distinct populations within ecotypes. Community structure within some ecotypes exhibited regular, seasonal patterns, but not for others, indicating other more irregular processes such as phage interactions are important. Network analysis including T4-like phage genotypic data revealed distinct viral variants correlated with different groups of cyanobacterial ASVs including time-lagged predator–prey relationships. Variation partitioning analysis indicated that phage community structure more strongly explains cyanobacterial community structure at the ASV level than the abiotic environmental factors. These results support a hierarchical model whereby abiotic environmental factors more strongly shape niche partitioning at the broader ecotype level while phage interactions are more important in shaping community structure of fine-scale variants within ecotypes.     

Identification of cultured and uncultured picocyanobacteria from a mesotrophic freshwater lake based on the partial sequences of 16S rDNA

Eight cultured strains (OK01, OK02, OK03, OK05, OK07, OK08, OK09, and OK10) of picocyanobacteria were isolated from Lake Okutama. Five cyanobacterial DNA fragments (DGGE bands; B4, B5, B6, B7, and B8) were obtained from the lake water samples by denaturing gradient gel electrophoresis (DGGE) after polymerase chain reaction (PCR) amplification of 16S ribosomal genes. To classify the picocyanobacterial strains and the DGGE bands, a partial sequence of 16S rDNA was used. Among seven strains, OK01, OK07, and OK09 were identified as the genus Synechococcus and OK02 and OK05 as the genus Phormidium. OK03 was identified as the genus Oscillatoria and was closely related to B4 (100% homology). B5, B6, B7, and B8 were related to the genus Synechococcus. These results revealed that the picocyanobacteria in the lake are phylogenetically diverse. PCR-DGGE analysis is a useful tool to determine picocyanobacterial community structure in freshwater environments. Received: February 25, 2001 / Accepted: July 27, 2001     

Discrete foraging niches promote ecological, phenotypic, and genetic divergence in sympatric whitefish (Coregonus lavaretus)

Natural populations often vary in their degree of ecological, morphological and genetic divergence. This variation can be arranged along an ecological speciation continuum of increasingly discrete variation, with high inter-individual variation at one end and well defined species in the other. In postglacial fishes, evolutionary divergence has commonly resulted in the co-occurrence of a pelagic and a benthic specialist. We studied three replicate lakes supporting sympatric pelagic and benthic European whitefish (Coregonus lavaretus (L.)) morphs in search for early signs of possible further divergence into more specialized niches. Using stomach content data (recent diet) and stable isotope analyses (time-integrated measure of trophic niche use), we observed a split in the trophic niche within the benthic whitefish morph, with individuals specializing on either littoral or profundal resources. This divergence in resource use was accompanied by small but significant differences in an adaptive morphological trait (gill raker number) and significant genetic differences between fish exploiting littoral and profundal habitats and foraging resources. The same pattern of parallel divergence was found in all three lakes, suggesting similar natural selection pressures driving and/or maintaining the divergence. The two levels of divergence (a clear and robust benthic – pelagic and a more subtle littoral – profundal divergence) observed in this study apparently represent different stages in the process of ecological speciation.     

Tracking differential incorporation of dissolved organic carbon types among diverse lineages of Sargasso Sea bacterioplankton

Bacterioplankton are the primary trophic conduit for dissolved organic carbon (DOC) and linking community structure with DOC utilization is central to understanding global carbon cycling. We coupled stable isotope probing (SIP) with 16S rRNA pyrosequencing in dark seawater culture experiments on euphotic and mesopelagic communities from the Sargasso Sea. Parallel cultures were amended with equimolar quantities of four DO¹³C substrates to simultaneously evaluate community utilization and population‐specific incorporation. Of the substrates tested – two cyanobacterial products (exudates or lysates from a culture of Synechococcus) and two defined monosaccharides (glucose or gluconic acid) – the cyanobacterial exudates were incorporated by the greatest diversity of oligotrophic bacterioplankton populations in surface waters, including taxa from > 10 major subclades within the Flavobacteria, Actinobacteria, Verrucomicrobia and Proteobacteria (including SAR11). In contrast, the monosaccharide glucose was not incorporated by any taxa belonging to extant oligotrophic oceanic clades. Conversely, proteobacterial copiotrophs, which were rare in the ambient water (< 0.1% of sequences), grew rapidly on all DOC amendments at both depths, but with different substrate preferences among lineages. We present a new analytical framework for using SIP to detect DOC incorporation across diverse oligotrophic bacterioplankton and discuss implications for the ecology of bacterial–DOC interactions among populations of diverging trophic strategies.     

Lack of congruence of genetic and niche divergence in Podarcis hispanicus complex

Niche divergence among closely related lineages can be informative on the ecological and evolutionary processes involved in differentiation, particularly in the case of cryptic species complexes. Here we compared phylogenetic relationships and niche similarity between pairs of lineages included in the Podarcis hispanicus complex to examine patterns of niche divergence and its role in the organization of current diversity patterns, as allopatric, parapatric, and sympatric lineages occur in the Western Mediterranean Basin. First, we used ecological niche models to characterize the realized climatic niche of each Podarcis hispanicus complex lineage based on topographic and climatic variables, to identify important variables, and to test for niche conservatism or divergence between pairs of lineages. Variables related to precipitation generally exhibited the highest contribution to niche models, highlighting the importance of rainfall levels in shaping distributions of Podarcis wall lizards. We found that most forms have significant differences in realized climatic niches that do not follow the pattern of mitochondrial divergence. These results lend support to the hypothesis that genetic divergence across Podarcis hispanicus complex most likely occurred in allopatric conditions, mostly with significant niche divergence. Competition after secondary contact is also suggested by the common occurrence of niche overlap between lineages that exhibit strictly parapatric distribution. The almost continuous distribution of Podarcis lizards in the study area appears to be a result of a combination of complementary suitable niches and competition, which seem two important mechanisms limiting geographic distributions and restricting the existence of extensive contact zones.     

Characterization of two Synechococcus sp. PCC7002‐related cyanobacterial strains in relation to 16S rDNA,crtR gene,lipids and pigments

Two Synechococcus strains from the Culture Collection of the Institute for Marine Sciences of Andalusia (Cádiz, Spain), namely Syn01 and Syn02, were found to be closely related to the model strain Synechococcus sp. PCC7002 according to 16S rDNA (99% identity). Pigment and lipid profiles and crtR genes of these strains were ascertained and compared. The sequences of the crtR genes of these strains were constituted by 888 bp, and showed 99% identity between Syn01 and Syn02, and 94% identity of Syn01 and Syn02 to Synechococcus sp. PCC7002. There was coincidence in photosynthetic pigments between the three strains apart from the pigment synechoxanthin, which could be only observed in Synechococcus sp. PCC7002. Species of sulfoquinovosyl‐diacyl‐glycerol (SQDG), phosphatidyl‐glycerol (PG), mono‐ and di‐galactosyl‐diacyl‐glycerol (MGDG and DGDG) were detected by high performance liquid chromatography‐mass spectrometry analysis of lipid extracts. The most abundant species within each lipid class were those containing C18:3 together with C16:0 fatty acyl substituents in the glycerol backbone of the same molecule. From these results it is concluded that these cyanobacterial strains belong to group 2 of the lipid classification of cyanobacteria.