Acetic acid bacteria encode two levansucrase types of different ecological relationship

Acetic acid bacteria (AAB) are associated with plants and insects. Determinants for the targeting and occupation of these widely different environments are unknown. However, most of these natural habitats share plant-derived sucrose, which can be metabolized by some AAB via polyfructose building levansucrases (LS) known to be involved in biofilm formation. Here, we propose two LS types (T) encoded by AAB as determinants for habitat selection, which emerged from vertical (T1) and horizontal (T2) lines of evolution and differ in their genetic organization, structural features and secretion mechanism, as well as their occurrence in proteobacteria. T1-LS are secreted by plant-pathogenic α- and γ-proteobacteria, while T2-LS genes are common in diazotrophic, plant-growth-promoting α-, β- and γ-proteobacteria. This knowledge may be exploited for a better understanding of microbial ecology, plant health and biofilm formation by sucrase-secreting proteobacteria in eukaryotic hosts.     

Microbial communities and organic biomarkers in a Proterozoic‐analog sinkhole

Little Salt Spring (Sarasota County, FL, USA) is a sinkhole with groundwater vents at ~77 m depth. The entire water column experiences sulfidic (~50 μM) conditions seasonally, resulting in a system poised between oxic and sulfidic conditions. Red pinnacle mats occupy the sediment–water interface in the sunlit upper basin of the sinkhole, and yielded 16S rRNA gene clones affiliated with Cyanobacteria, Chlorobi, and sulfate‐reducing clades of Deltaproteobacteria. Nine bacteriochlorophyll e homologues and isorenieratene indicate contributions from Chlorobi, and abundant chlorophyll a and pheophytin a are consistent with the presence of Cyanobacteria. The red pinnacle mat contains hopanoids, including 2‐methyl structures that have been interpreted as biomarkers for Cyanobacteria. A single sequence of hpnP, the gene required for methylation of hopanoids at the C‐2 position, was recovered in both DNA and cDNA libraries from the red pinnacle mat. The hpnP sequence was most closely related to cyanobacterial hpnP sequences, implying that Cyanobacteria are a source of 2‐methyl hopanoids present in the mat. The mats are capable of light‐dependent primary productivity as evidenced by ¹³C‐bicarbonate photoassimilation. We also observed ¹³C‐bicarbonate photoassimilation in the presence of DCMU, an inhibitor of electron transfer to Photosystem II. Our results indicate that the mats carry out light‐driven primary production in the absence of oxygen production—a mechanism that may have delayed the oxygenation of the Earth's oceans and atmosphere during the Proterozoic Eon. Furthermore, our observations of the production of 2‐methyl hopanoids by Cyanobacteria under conditions of low oxygen and low light are consistent with the recovery of these structures from ancient black shales as well as their paucity in modern marine environments.     

Potential for <Emphasis Type="Italic">luxS</Emphasis> related signalling in marine bacteria and production of autoinducer-2 in the genus <Emphasis Type="Italic">Shewanella</Emphasis>

Background  

The autoinducer-2 (AI-2) group of signalling molecules are produced by both Gram positive and Gram negative bacteria as the by-product of a metabolic transformation carried out by the LuxS enzyme. They are the only non species-specific quorum sensing compounds presently known in bacteria. The luxS gene coding for the AI-2 synthase enzyme was found in many important pathogens. Here, we surveyed its occurrence in a collection of 165 marine isolates belonging to abundant marine phyla using conserved degenerated PCR primers and sequencing of selected positive bands to determine if the presence of the luxS gene is phylogenetically conserved or dependent on the habitat.     

Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche

Molecular fossils of 2-methylhopanoids are prominent biomarkers in modern and ancient sediments that have been used as proxies for cyanobacteria and their main metabolism, oxygenic photosynthesis. However, substantial culture and genomic-based evidence now indicates that organisms other than cyanobacteria can make 2-methylhopanoids. Because few data directly address which organisms produce 2-methylhopanoids in the environment, we used metagenomic and clone library methods to determine the environmental diversity of hpnP, the gene encoding the C-2 hopanoid methylase. Here we show that hpnP copies from alphaproteobacteria and as yet uncultured organisms are found in diverse modern environments, including some modern habitats representative of those preserved in the rock record. In contrast, cyanobacterial hpnP genes are rarer and tend to be localized to specific habitats. To move beyond understanding the taxonomic distribution of environmental 2-methylhopanoid producers, we asked whether hpnP presence might track with particular variables. We found hpnP to be significantly correlated with organisms, metabolisms and environments known to support plant–microbe interactions (P-value<10⁻⁶); in addition, we observed diverse hpnP types in closely packed microbial communities from other environments, including stromatolites, hot springs and hypersaline microbial mats. The common features of these niches indicate that 2-methylhopanoids are enriched in sessile microbial communities inhabiting environments low in oxygen and fixed nitrogen with high osmolarity. Our results support the earlier conclusion that 2-methylhopanoids are not reliable biomarkers for cyanobacteria or any other taxonomic group, and raise the new hypothesis that, instead, they are indicators of a specific environmental niche.     

Assessing the distribution of sedimentary C40 carotenoids through time

A comprehensive marine biomarker record of green and purple sulfur bacteria (GSB and PSB, respectively) is required to test whether anoxygenic photosynthesis represented a greater fraction of marine primary productivity during the Precambrian than the Phanerozoic, as current models of ocean redox evolution suggest. For this purpose, we analyzed marine rock extracts and oils from the Proterozoic to the Paleogene for C₄₀ diagenetic products of carotenoid pigments using new analytical methods. Gas chromatography coupled with tandem mass spectrometry provides a new perspective on the temporal distributions of carotenoid biomarkers for phototrophic sulfur bacteria, specifically okenane, chlorobactane, and paleorenieratane. According to conventional paleoredox interpretations, this revised stratigraphic distribution of the GSB and PSB biomarkers implies that the shallow sunlit surface ocean (<24 m) became sulfidic more frequently in the geologic past than was previously thought. We reexamine whether there is evidence supporting a planktonic source of GSB and PSB pigments in marine systems or whether additional factors are required to explain the marine phototrophic sulfur bacteria record. To date, planktonic GSB and PSB and their pigments have been identified in restricted basins and lakes, but they have yet to be detected in the unrestricted, transiently sulfidic, marine systems. Based on modern observations, additional environmental factors, including basin restriction, microbial mats, or sediment transport, may be required to fully explain GSB and PSB carotenoids in the geologic record.     

Phylogenetic diversity and characterization of 2-haloacid degrading bacteria from the marine sponge <Emphasis Type="Italic">Hymeniacidon perlevis</Emphasis>

A total of 139 2-haloacid degrading bacteria strains were isolated from the marine sponge Hymeniacidon perlevis using a modified enrichment medium and a pH indicator method. After screening on indicator agar and 2-chloropropionic acid (2-CPA) liquid medium, 11 isolates with high degrading activities were characterized and initially identified. Seven of the 11 isolates were able to degrade 2-CPA at 8% salt, and four isolates (DEH 66, DEH 99, DEH125 and DEH138) degraded 2-CPA at 15% salt. Eight of the 11 isolates utilized all four types of organohalogen compounds used in this study. The DEH99 and DEH138 isolates exhibited the best enantioselectivity towards (S)-2-chloropropionic acid (S-CPA) and (R)-2-chloropropionic acid (R-CPA), respectively. The dehalogenase activities of DEH84 against racemic CPA, DEH99 against S-CPA, DEH138 against R-CPA and DEH130 against racemic CPA were 0.16U/mg, 0.06U/mg, 0.12U/mg and 0.19U/mg, respectively. Based on 16S rRNA sequence analysis, the 11 isolates were clustered into the Rhodobacteraceae family of α-proteobacteria and the Pseudomonadaceae family of γ-proteobacteria. To our knowledge, this is the first report detailing the isolation of organisms of Pseudomonas stuzeri sp. and the Rhodobacteraceae family with 2-haloacid dehalogenase activity from marine sponges.     

Pacific Northwest Marine Sediments Contain Ammonia-Oxidizing Bacteria in the β Subdivision of the Proteobacteria

The diversity of ammonia-oxidizing bacteria in aquatic sediments was studied by retrieving ammonia monooxygenase and methane monooxygenase gene sequences. Methanotrophs dominated freshwater sediments, while β-proteobacterial ammonia oxidizers dominated marine sediments. These results suggest that γ-proteobacteria such as Nitrosococcus oceani are minor members of marine sediment ammonia-oxidizing communities.     

Population structure within an alpine archipelago: strong signature of past climate change in the New Zealand rock wren (Xenicus gilviventris)

Naturally subdivided populations such as those occupying high‐altitude habitat patches of the ‘alpine archipelago’ can provide significant insight into past biogeographical change and serve as useful models for predicting future responses to anthropogenic climate change. Among New Zealand's alpine taxa, phylogenetic studies support two major radiations: the first correlating with geological forces (Pliocene uplift) and the second with climatic processes (Pleistocene glaciations). The rock wren (Xenicus gilviventris) is a threatened alpine passerine belonging to the endemic New Zealand wren family (Acanthisittidae). Rock wren constitute a widespread, naturally fragmented population, occurring in patches of suitable habitat over c. 900 m in altitude throughout the length of the South Island, New Zealand. We investigated the relative role of historical geological versus climatic processes in shaping the genetic structure of rock wren (N = 134) throughout their range. Using microsatellites combined with nuclear and mtDNA sequence data, we identify a deep north–south divergence in rock wren (3.7 ± 0.5% at cytochrome b) consistent with the glacial refugia hypothesis whereby populations were restricted in isolated refugia during the Pleistocene c. 2 Ma. This is the first study of an alpine vertebrate to test and provide strong evidence for the glacial refugia hypothesis as an explanation for the low endemicity central zone known as the biotic ‘gap’ in the South Island of New Zealand.     

Historical perspectives on population genetics and conservation of three marine turtle species

Considerable phylogeographic and population genetic research has been conducted on marine turtles. Less attention, however, has been paid to the historical patterns and processes that have led to present patterns of genetic structure, and particularly, how these populations have responded to major climatic changes in the past. To address these questions, we analyzed previously published mitochondrial haplotype data independently for three marine turtle species, the loggerhead (Caretta caretta), hawksbill (Eretmochelys imbricata), and green turtle (Chelonia mydas). Considering all three species, we conducted analyses on a total of 657 individuals from 36 nesting beaches in the Atlantic and Mediterranean. Our results suggest that much of the contemporary genetic structure has been significantly affected by complex patterns of historical population subdivision, long-distance dispersal, and restricted geneflow. These inferences also imply that the climatic and sea level fluctuations during the Pleistocene may have had contrasting effects on genetic structure (e.g., fragmenting versus homogenizing) and on population sizes. Estimates of historical and current effective population sizes further highlight differential demographic responses across species to historical climatic cycles. Collectively, our results provide evidence for the occurrence of historical refugia through climatic cycles and complex historical metapopulation dynamics, and identify common and unique patterns of metapopulation structure across species. These historical patterns provide a basis for predictive estimates of metapopulation responses to habitat loss, population extirpation, and global climatic change.     

Relationship between the alpha diversity of communities and the appearance rates of new genera in the evolution of phanerozoic marine biota

The influence of the alpha diversity of communities on the appearance rates of new species may be either positive (due to coevolution and niche construction) or negative (due to community saturation). The development of global paleontological databases allows the extrapolation of the analysis of these effects to past geological epochs. To assess the effect of alpha diversity on the rates of generic formation in the evolution of the Phanerozoic marine biota, the correlation of the parameters D (mean generic diversity of paleontological collections containing representatives of a large taxon) and B (relative rate of the appearance of new genera in the given large taxon) was analyzed. The majority of large taxa, and the Phanerozoic biota in general, characteristically show predominance of periods of positive correlation (synchronous changes) of B and D, separated by shorter periods of negative correlation (opposite phase changes). These can be interpreted as periods of positive and negative influence of alpha diversity on diversification, although positive correlation can be generated by other factors, including taphonomic ones. Apparently, in the evolution of the Phanerozoic marine biota, the coevolution and “niche construction” played a more significant role than the effect of “saturation” of communities.     

Early response of the platypus to climate warming

Combining a climatic envelope modelling technique with more than two centuries (1800–2009) of distribution records has revealed the effects of a changing climate on the egg‐laying monotreme, the platypus, Ornithorhynchus anatinus. We show that the main factor associated with platypus occurrence switched from aquatic habitat availability (estimated by rainfall) to thermal tolerances (estimated by annual maximum temperature) in the 1960s. This correlates directly with the change in the annual maximum temperature anomaly from cooler to warmer conditions in southeastern Australia. Modelling of platypus habitat under emission scenarios (A1B, A2, B1 and B2) revealed large decreases (>30%) in thermally suitable habitat by 2070. This reduction, compounded by increasing demands for water for agriculture and potable use, suggests that there is real cause for concern over the future status of this species, and highlights the need for restoration of thermal refugia within the platypus’ modelled range.     

Patterns of generic extinction in the fossil record

Analysis of the stratigraphic records of 19,897 fossil genera indicates that most classes and orders show largely congruent rises and falls in extinction intensity throughout the Phanerozoic. Even an ecologically homogeneous sample of reef genera shows the same basic extinction profile. The most likely explanation for the congruence is that extinction is physically rather than biologically driven and that it is dominated by the effects of geographically widespread environmental perturbations influencing most habitats. Significant departures from the congruence are uncommon but important because they indicate physiological or habitat selectivity. The similarity of the extinction records of reef organisms and the marine biota as a whole confirms that reefs and other faunas are responding to the same history of environmental stress.     

Identification of Diazotrophs in the Culturable Bacterial Community Associated with Roots of <Emphasis Type="Italic">Lasiurus sindicus</Emphasis>, a Perennial Grass of Thar Desert,India

Lasiurus sindicus is a highly nutritive, drought-tolerant, perennial grass that is endemic to the Thar Desert of Rajasthan, India. Analysis of 16S rRNA coding genes of the bacterial isolates enriched in nitrogen-free semisolid medium, from the surface-sterilized roots of L. sindicus, showed predominance of Gram-negative over Gram-positive bacteria. According to comparative sequence analysis of 16S rDNA sequence data, Gram-positive bacteria with low GC content (Staphylococcus warneri and Bacillus sp.) and high GC content (Micrococcus luteus, Microbacterium sp.) were identified. Gram-negative bacteria included Azospirillum sp., Rhizobium sp., Agrobacterium tumefaciens, and Inquilinus limosus (α-proteobacteria); Ralstonia sp., Variovorax paradoxus, and Bordetella petrii (β-proteobacteria); and Pseudomonas pseudoalcaligenes, Stenotrophomonas sp. (γ-proteobacteria). The occurrence of nifH sequences in Azospirillum sp., Rhizobium sp., and P. pseudoalcaligenes showed the possibility of supplying biologically fixed nitrogen by the root-associated diazotrophs to the host plant.     

Habitat effects and sampling bias on Phanerozoic reef distribution

Incomplete preservation, heterogeneous geographic sampling, uncertainties in palaeogeographic reconstructions and inconsistencies of reef definitions bias global reef patterns observed in the geological record. This sampling bias is added to a biological habitat area effect, which is thought to be of paramount importance for modern reefs. To evaluate the importance of sampling bias of ancient reefs, I first tested the habitat area effect and sampling bias for modern tropical reefs and then evaluated these factors for pre-Pleistocene Phanerozoic reefs. Results suggest that habitat area, although significantly affecting Phanerozoic reef patterns, is considerably less important than sampling bias. Sampling bias is more controlled by socioeconomic factors than by geological processes such as subduction of oceanic crust or sea-level fluctuations. Reefs are more likely to be sampled in rich countries, irrespective of geological and ecological controls. The numeric and geographic distribution of reefs as currently recorded in the published literature is thus probably largely artifactual, which may explain the scarcity of significant correlations between reef distribution patterns and inferred physico-chemical controls.     

Changes in lifestyle and habitat of Zoophycos‐producing animals related to evolution of phytoplankton during the Late Mesozoic: geological evidence for the ‘benthic‐pelagic coupling model’

The trace fossil Zoophycos characterized by complex, three‐dimensional morphology with systematic internal structures occurs throughout the Phanerozoic marine sediments. The specimens of Zoophycos examined herein consist of a downward and helical spreite and are a product of the excretory behaviour of endobenthic detritus feeders. They are divided into two basic types: pre‐Jurassic and post‐Cretaceous types on the basis of whorls of spreiten in a single specimen. The pre‐Jurassic type has fewer than four whorls. In contrast, most of the post‐Cretaceous specimens exhibit spreite with multiple coils more than ten whorls. The abrupt increase in whorl number during the Cretaceous suggests that the sedentary lifestyle of the producer should change from a short‐term stay to long‐term or permanent occupation of the same burrow. Timing of the lifestyle change the Zoophycos producers seems to be closely related to the deep‐seaward migration of their habitats. The change in lifestyle and migration of Zoophycos‐producing animals during the Cretaceous might be attributable to the establishment of eutrophic bottom conditions in the deep sea. These changes seem to be associated with the flux of large amounts of phytodetrital food produced by phytoplankton, which experienced an explosive increase in species diversity during the Late Jurassic to the Late Cretaceous. The series of changes in lifestyle and habitat of the Zoophycos animals during the Late Mesozoic can serve as one piece of geological evidence for the ‘benthic‐pelagic coupling model’.     

Predation by the Ordovician asteroid Promopalaeaster on a pelecypod

Blake, D.B. & Guensburg, T.E. 1994 10 15: Predation by the Ordovician asteroid Promopalaeaster on a pelecypod. An Ordovician Prornopalaeaster (Echinodermata: Asteroidea) wrapped about a Cuneamya? (Mol-lusca: Pelecypoda) in the extraoral feeding posture characteristic of Jurassic to modern members of the Asteriidae documents an early origin for this behavioral complex. Modern asteriids are convergent on Promopalaeastet; there is no direct phylogenetic linkage between the two. This fossil occurrence, combined with the success of modem Asteriidae, demonstrates that biological evolution and geological change need not outmode complex life habits. The fossil supports the notion of asteroids as Paleozoic-type predators, and its existence suggests that asteroids were not significant contributors to changing faunal structures in shelf seas during the Phanerozoic. Asteroidea, Pelecypoda, functional morphology, evolutionary ecology.     

Spatial segregation of sympatric marten and fishers: the influence of landscapes and species‐scapes

Co‐occurring species are rarely considered as a factor influencing habitat selection. However, niche theory predicts that sharing resources, predators, and other interspecific interactions can limit the environmental conditions under which a species may exist. How does the spatial distribution of one species affect that of another within shared landscapes? We tested whether sympatric marten Martes americana and fishers M. pennanti in a mountain landscape in Alberta, Canada exhibit local‐scale spatial segregation, beyond differential habitat selection. We modelled marten and fisher distribution in relation to remotely‐sensed habitat data and species co‐occurrence, using generalized linear models and information‐theoretic model selection. Marten and fishers selected different habitat types and showed different responses to habitat fragmentation. Even after accounting for these differences, the absence of one species significantly explained the occurrence of the other. We conclude that the spatial distribution of marten and fishers influences habitat selection by each other at landscape scales, and hypothesize that this pattern may result from competition in a spatially heterogeneous environment. Species‐habitat models that consider only resources may fail to capture key predictors of species’ occurrence. Reliable prediction and inference requires that ecologists expand from landscapes to also include species‐scapes: a spatial plane of species interactions that combines with resources to drive species’ distributions.     

Differential Growth Response of Colony-Forming α- and γ-Proteobacteria in Dilution Culture and Nutrient Addition Experiments from Lake Kinneret (Israel), the Eastern Mediterranean Sea, and the Gulf of Eilat

Even though it is widely accepted that bacterioplankton growth in lakes and marine ecosystems is determined by the trophic status of the systems, knowledge of the relationship between nutrient concentrations and growth of particular bacterial species is almost nonexistent. To address this question, we performed a series of culture experiments with water from Lake Kinneret (Israel), the eastern Mediterranean Sea, and the Gulf of Eilat (northern Red Sea). In the initial water samples, the proportion of CFU was typically <0.002% of the 4′,6′-diamidino-2-phenylindole (DAPI) counts. During incubation until the early stationary phase, the proportion of CFU increased to 20% of the DAPI counts and to 2 to 15% of the DAPI counts in unenriched lake water and seawater dilution cultures, respectively. Sequencing of the 16S ribosomal DNA of colony-forming bacteria in these cultures consistently revealed an abundance of α-proteobacteria, but notable phylogenetic differences were found at the genus level. Marine dilution cultures were dominated by bacteria in the Roseobacter clade, while lake dilution cultures were dominated by bacteria affiliated with the genera Sphingomonas and Caulobacter. In nutrient (glucose, ammonium, phosphate) addition experiments the CFU comprised 20 to 83% of the newly grown cells. In these incubation experiments fast-growing γ-proteobacteria dominated; in the marine experiments primarily different Vibrio and Alteromonas species appeared, while in the lake water experiments species of the genera Shewanella, Aeromonas, and Rheinheimera grew. These results suggest that major, but different, γ-proteobacterial genera in both freshwater and marine environments have a preference for elevated concentrations of nutrients and easily assimilated organic carbon sources but are selectively outcompeted by α-proteobacteria in the presence of low nutrient concentrations.     

Ecology of tropical marine fungi

Lignicolous material was collected from 5 marine locations in Brunei: a rocky headland, a sandy beach, a man-made brackish lake, a healthy mangrove and an oil polluted mangrove. Higher marine fungi present were identified and their percentage occurrence noted. The common marine fungi varied from habitat to habitat. Antennospora quadricornuta was most common at the rocky headland, Corollospora pulchella at the sandy beach and Halosarpheia marina at the brackish lake. In the mangroves the most common species were Halocyphina villosa (healthy) and Cirrenalia pygmea and Lulworthia grandispora (oil polluted). Differences in species composition from one habitat to the next were observed, although some fungi occurred throughout. There were significantly less diversity and numbers of fungi in the oil polluted mangrove when compared to the healthy mangrove. Observations concerning the ecology of tropical marine fungi are made.