Microbial mat controls on infaunal abundance and diversity in modern marine microbialites

Microbialites are the most abundant macrofossils of the Precambrian. Decline in microbialite abundance and diversity during the terminal Proterozoic and early Phanerozoic has historically been attributed to the concurrent radiation of complex metazoans. Similarly, the apparent resurgence of microbialites in the wake of Paleozoic and Mesozoic mass extinctions is frequently linked to drastic declines in metazoan diversity and abundance. However, it has become increasing clear that microbialites are relatively common in certain modern shallow, normal marine carbonate environments—foremost the Bahamas. For the first time, we present data, collected from the Exuma Cays, the Bahamas, systematically characterizing the relationship between framework‐building cyanobacteria, microbialite fabrics, and microbialite‐associated metazoan abundance and diversity. We document the coexistence of diverse microbialite and infaunal metazoan communities and demonstrate that the predominant control upon both microbialite fabric and metazoan community structure is microbial mat type. These findings necessitate that we rethink prevalent interpretations of microbialite–metazoan interactions and imply that microbialites are not passive recipients of metazoan‐mediated alteration. Additionally, this work provides support for the theory that certain Precambrian microbialites may have been havens of early complex metazoan life, rather than bereft of metazoans, as has been traditionally envisaged.     

Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar,Mexico

Laguna Bacalar is a sulfate‐rich freshwater lake on the Yucatan Peninsula that hosts large microbialites. High sulfate concentrations distinguish Laguna Bacalar from other freshwater microbialite sites such as Pavilion Lake and Alchichica, Mexico, as well as from other aqueous features on the Yucatan Peninsula. While cyanobacterial populations have been described here previously, this study offers a more complete characterization of the microbial populations and corresponding biogeochemical cycling using a three‐pronged geobiological approach of microscopy, high‐throughput DNA sequencing, and lipid biomarker analyses. We identify and compare diverse microbial communities of Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria that vary with location along a bank‐to‐bank transect across the lake, within microbialites, and within a neighboring mangrove root agglomeration. In particular, sulfate‐reducing bacteria are extremely common and diverse, constituting 7%–19% of phylogenetic diversity within the microbialites, and are hypothesized to significantly influence carbonate precipitation. In contrast, Cyanobacteria account for less than 1% of phylogenetic diversity. The distribution of lipid biomarkers reflects these changes in microbial ecology, providing meaningful biosignatures for the microbes in this system. Polysaturated short‐chain fatty acids characteristic of cyanobacteria account for <3% of total abundance in Laguna Bacalar microbialites. By contrast, even short‐chain and monounsaturated short‐chain fatty acids attributable to both Cyanobacteria and many other organisms including types of Alphaproteobacteria and Gammaproteobacteria constitute 43%–69% and 17%–25%, respectively, of total abundance in microbialites. While cyanobacteria are the largest and most visible microbes within these microbialites and dominate the mangrove root agglomeration, it is clear that their smaller, metabolically diverse associates are responsible for significant biogeochemical cycling in this microbialite system.     

The importance of groundwater flow to the formation of modern thrombolitic microbialites

Modern microbialites are often located within groundwater discharge zones, yet the role of groundwater in microbialite accretion has yet to be resolved. To understand relationships between groundwater, microbialites, and associated microbial communities, we quantified and characterized groundwater flow and chemistry in active thrombolitic microbialites in Lake Clifton, Western Australia, and compared these observations to inactive thrombolites and lakebed sediments. Groundwater flows upward through an interconnected network of pores within the microstructure of active thrombolites, discharging directly from thrombolite heads into the lake. This upwelling groundwater is fresher than lake water and is hypothesized to support microbial mat growth by reducing salinity and providing limiting nutrients in an osmotically stressful and oligotrophic habitat. This is in contrast to inactive thrombolites that show no evidence of microbial mat colonization and are infiltrated by hypersaline lake water. Groundwater discharge through active thrombolites contrasts with the surrounding lakebed, where hypersaline lake water flows downward through sandy sediments at very low rates. Based on an appreciation for the role of microorganisms in thrombolite accretion, our findings suggest conditions favorable to thrombolite formation still exist in certain locations of Lake Clifton despite increasing lake water salinity. This study is the first to characterize groundwater flow rates, paths, and chemistry within a microbialite‐forming environment and provides new insight into how groundwater can support microbial mats believed to contribute to microbialite formation in modern and ancient environments.     

Cyanobacterial diversity in the phyllosphere of a mangrove forest

The cyanobacterial community colonizing phyllosphere in a well-preserved Brazilian mangrove ecosystem was assessed using cultivation-independent molecular approaches. Leaves of trees that occupy this environment (Rhizophora mangle,Avicennia schaueriana and Laguncularia racemosa) were collected along a transect beginning at the margin of the bay and extending upland. The results demonstrated that the phyllosphere of R. mangle and L. racemosa harbor similar assemblages of cyanobacteria at each point along the transect. A. schaueriana, found only in the coastal portions of the transect, was colonized by assemblages with lower richness than the other trees. However, the results indicated that spatial location was a stronger driver of cyanobacterial community composition than plant species. Distinct cyanobacterial communities were observed at each location along the coast-to-upland transect. Clone library analysis allowed identification of 19 genera of cyanobacteria and demonstrated the presence of several uncultivated taxa. A predominance of sequences affiliated with the orders Nostocales and Oscillatoriales was observed, with a remarkable number of sequences similar to genera Symphyonemopsis/Brasilonema (order Nostocales). The results demonstrated that phyllosphere cyanobacteria in this mangrove forest ecosystem are influenced by environmental conditions as the primary driver at the ecosystem scale, with tree species exerting some effect on community structure at the local scale.     

Cyanobacterial diversity in the rhizosphere of rice and its ecological significance

This investigation was undertaken to characterize the abundance and genera-wise diversity of cyanobacteria in the rice rhizosphere and nitrogen-fixing ability of the isolated strains. The cyanobacterial strains belonging to the genera Nostoc and Anabaena comprised 80% of the rhizosphere isolates, which were also efficient in enhancing the germination and growth of wheat seeds and exhibited significantly high protein accumulation and IAA production. Distinct profiles for the cyanobacterial strains were obtained on amplification with extended Hip 1 primer — HipTG, indicative of the diversity among these strains. Our investigation helped in identifying promising cyanobacterial isolates from the rhizosphere of rice, which can be utilized in developing efficient plant growth promoting cyanobacterial inoculants.     

Biogeochemical cycling and microbial diversity in the thrombolitic microbialites of Highborne Cay,Bahamas

Thrombolites are unlaminated carbonate build‐ups that are formed via the metabolic activities of complex microbial mat communities. The thrombolitic mats of Highborne Cay, Bahamas develop in close proximity (1–2 m) to accreting laminated stromatolites, providing an ideal opportunity for biogeochemical and molecular comparisons of these two distinctive microbialite ecosystems. In this study, we provide the first comprehensive characterization of the biogeochemical activities and microbial diversity of the Highborne Cay thrombolitic mats. Morphological and molecular analyses reveal two dominant mat types associated with the thrombolite deposits, both of which are dominated by bacteria from the taxa Cyanobacteria and Alphaproteobacteria. Diel cycling of dissolved oxygen (DO) and dissolved inorganic carbon (DIC) were measured in all thrombolitic mat types. DO production varied between thrombolitic types and one morphotype, referred to in this study as ‘button mats’, produced the highest levels among all mat types, including the adjacent stromatolites. Characterization of thrombolite bacterial communities revealed a high bacterial diversity, roughly equivalent to that of the nearby stromatolites, and a low eukaryotic diversity. Extensive phylogenetic overlap between thrombolitic and stromatolitic microbial communities was observed, although thrombolite‐specific cyanobacterial populations were detected. In particular, the button mats were dominated by a calcified, filamentous cyanobacterium identified via morphology and 16S rRNA gene sequencing as Dichothrix sp. The distinctive microbial communities and chemical cycling patterns within the thrombolitic mats provide novel insight into the biogeochemical processes related to the lithifying mats in this system, and provide data relevant to understanding microbially induced carbonate biomineralization.     

Cyanobacterial diversity and a new acaryochloris-like symbiont from Bahamian sea-squirts

Symbiotic interactions between ascidians (sea-squirts) and microbes are poorly understood. Here we characterized the cyanobacteria in the tissues of 8 distinct didemnid taxa from shallow-water marine habitats in the Bahamas Islands by sequencing a fragment of the cyanobacterial 16S rRNA gene and the entire 16S-23S rRNA internal transcribed spacer region (ITS) and by examining symbiont morphology with transmission electron (TEM) and confocal microscopy (CM). As described previously for other species, Trididemnum spp. mostly contained symbionts associated with the Prochloron-Synechocystis group. However, sequence analysis of the symbionts in Lissoclinum revealed two unique clades. The first contained a novel cyanobacterial clade, while the second clade was closely associated with Acaryochloris marina. CM revealed the presence of chlorophyll d (chl d) and phycobiliproteins (PBPs) within these symbiont cells, as is characteristic of Acaryochloris species. The presence of symbionts was also observed by TEM inside the tunic of both the adult and larvae of L. fragile, indicating vertical transmission to progeny. Based on molecular phylogenetic and microscopic analyses, Candidatus Acaryochloris bahamiensis nov. sp. is proposed for this symbiotic cyanobacterium. Our results support the hypothesis that photosymbiont communities in ascidians are structured by host phylogeny, but in some cases, also by sampling location.     

Cyanobacterial assimilatory nitrate reductase gene diversity in coastal and oligotrophic marine environments

Cyanobacteria are important primary producers in many marine ecosystems and their abundances and growth rates depend on their ability to assimilate various nitrogen sources. To examine the diversity of nitrate-utilizing marine cyanobacteria, we developed PCR primers specific for cyanobacterial assimilatory nitrate reductase (narB) genes. We obtained amplification products from diverse strains of cultivated cyanobacteria and from several marine environments. Phylogenetic trees constructed with the narB gene are congruent with those based on ribosomal RNA genes and RNA polymerase genes. Analysis of sequence library data from coastal and oligotrophic marine environments shows distinct groups of Synechococcus sp. in each environment; some of which are represented by sequences from cultivated organisms and others that are unrelated to known sequences and likely represent novel phylogenetic groups. We observed spatial differences in the distribution of sequences between two sites in Monterey Bay and differences in the vertical distribution of sequence types at the Hawai'i Ocean Time-series Station ALOHA, suggesting that nitrogen assimilation in Synechococcus living in different ecological niches can be followed with the nitrate reductase gene.     

Cyanobacterial diversity in geographically related and distant host plants of the genus Gunnera

The diversity among 45 cyanobacterial isolates from 11 different Gunnera species originating from different geographical areas was examined. By means of polymerase chain reaction (PCR) fingerprinting with short tandemly repeated repetitive (STRR) sequences as primers, ten groups of symbiotic cyanobacteria and five unique isolates not belonging to a particular group were identified. Most groups were restricted to one geographical area, indicating a limited distribution of related cyanobacterial strains. An extensive cyanobacterial diversity was found both within and between the 11 different Gunnera species. Within a particular plant and even within the same stem gland, more than one cyanobacterial strain at a time could be present. These results indicate a low specificity in Gunnera-Nostoc symbiosis.     

铜陵铜尾矿废弃地生物土壤结皮中的蓝藻多样性

生物土壤结皮是生态系统原生演替过程中的一个早期阶段,在铜陵铜尾矿废弃地自然生态恢复过程中生物土壤结皮在尾矿废弃地表面广泛分布.以生长在铜陵杨山冲和铜官山2处铜尾矿废弃地的生物土壤结皮为研究对象,运用常规培养方法和变性梯度凝胶电泳技术(PCR-DGGE)对不同群落生物土壤结皮中的蓝藻多样性及优势类群进行研究.结果表明2种研究方法所获得的蓝藻种类组成具有明显差异.显微观察结果表明常规培养试验中主要蓝藻类群为微囊藻属(Microcystis)、色球藻属(Chroococcus)、颤藻属(Oscillatoria)、念珠藻属(Nostoc)和浮鞘丝藻属(Planktolyngbya),其中优势种类主要为铜绿微囊藻(Microcystis aeruginosa)、断裂颤藻(Oscillatoria fracta)和细浮鞘丝藻(Planktolyngbya subtilis);提取样品中微生物总DNA,对蓝藻16SrRNA进行PCR-DGGE分析,回收DGGE图谱中24个条带进行测序分析,结果显示,所有序列与GenBank数据库中的近缘蓝藻的相似性系数均在93％以上,其中优势蓝藻类群主要隶属于微鞘藻属(Microcoleus)和细鞘丝藻属(Leptolyngbya),裸地(YL)处和木贼群落下尾矿表面(YM)的生物土壤结皮中优势蓝藻类群主要为微鞘藻属,而黄色真藓-藻类混合结皮(YT)和白茅群落( YB,TG)下的生物土壤结皮中的优势类群主要隶属于细鞘丝藻属.     

Bacterial diversity and carbonate precipitation in the giant microbialites from the highly alkaline Lake Van, Turkey

Lake Van harbors the largest known microbialites on Earth. The surface of these huge carbonate pinnacles is covered by coccoid cyanobacteria whereas their central axis is occupied by a channel through which neutral, relatively Ca-enriched, groundwater flows into highly alkaline (pH ~9.7) Ca-poor lake water. Previous microscopy observations showed the presence of aragonite globules composed by rounded nanostructures of uncertain origin that resemble similar bodies found in some meteorites. Here, we have carried out fine-scale mineralogical and microbial diversity analyses from surface and internal microbialite samples. Electron transmission microscopy revealed that the nanostructures correspond to rounded aragonite nanoprecipitates. A progressive mineralization of cells by the deposition of nanoprecipitates on their surface was observed from external towards internal microbialite areas. Molecular diversity studies based on 16S rDNA amplification revealed the presence of bacterial lineages affiliated to the Alpha-, Beta- and Gammaproteobacteria, the Cyanobacteria, the Cytophaga-Flexibacter-Bacteroides (CFB) group, the Actinobacteria and the Firmicutes. Cyanobacteria and CFB members were only detected in surface layers. The most abundant and diverse lineages were the Firmicutes (low GC Gram positives). To the exclusion of cyanobacteria, the closest cultivated members to the Lake Van phylotypes were most frequently alkaliphilic and/or heterotrophic bacteria able to degrade complex organics. These heterotrophic bacteria may play a crucial role in the formation of Lake Van microbialites by locally promoting carbonate precipitation.     

Cyanobacterial two-component proteins: structure, diversity, distribution, and evolution.

A survey of the already characterized and potential two-component protein sequences that exist in the nine complete and seven partially annotated cyanobacterial genome sequences available (as of May 2005) showed that the cyanobacteria possess a much larger repertoire of such proteins than most other bacteria. By analysis of the domain structure of the 1,171 potential histidine kinases, response regulators, and hybrid kinases, many various arrangements of about thirty different modules could be distinguished. The number of two-component proteins is related in part to genome size but also to the variety of physiological properties and ecophysiologies of the different strains. Groups of orthologues were defined, only a few of which have representatives with known physiological functions. Based on comparisons with the proposed phylogenetic relationships between the strains, the orthology groups show that (i) a few genes, some of them clustered on the genome, have been conserved by all species, suggesting their very ancient origin and an essential role for the corresponding proteins, and (ii) duplications, fusions, gene losses, insertions, and deletions, as well as domain shuffling, occurred during evolution, leading to the extant repertoire. These mechanisms are put in perspective with the different genetic properties that cyanobacteria have to achieve genome plasticity. This review is designed to serve as a basis for orienting further research aimed at defining the most ancient regulatory mechanisms and understanding how evolution worked to select and keep the most appropriate systems for cyanobacteria to develop in the quite different environments that they have successfully colonized.     

Occurrence and diversity of lipids in modern coral skeletons

Coral skeletons are composite acellular structures, in which organic macromolecules are intimately associated with mineral phases. Previous studies focussed on proteins and sugars of the soluble organic matrices extracted from the skeletons. Here we report the occurrence of diverse lipids which were extracted from the aragonitic skeletons of seven modern coral species. Using thin layer chromatography, we show that these lipids differ in quantity and composition between the species. Higher proportions of sterols and sterol esters in skeleton extracts as compared to a much higher abundance of waxes and triglycerides in previously studied extracts from scleractinian soft tissues suggest a specific, although not yet determined, role in biomineralisation. The occurrence of intraskeletal lipids along with other organic components should also be taken into account when using coral skeletons as bone allografts, as well as in fossilisation processes.     

Cyanobacterial diversity in extreme environments in Baja California, Mexico: a polyphasic study

Cyanobacterial diversity from two geographical areas of Baja California Sur, Mexico, were studied: Bahia Concepcion, and Ensenada de Aripez. The sites included hypersaline ecosystems, sea bottom, hydrothermal springs, and a shrimp farm. In this report we describe four new morphotypes, two are marine epilithic from Bahia Concepcion, Dermocarpa sp. and Hyella sp. The third, Geitlerinema sp., occurs in thermal springs and in shrimp ponds, and the fourth, Tychonema sp., is from a shrimp pond. The partial sequences of the 16S rRNA genes and the phylogenetic relationship of four cyanobacterial strains (Synechococcus cf. elongatus, Leptolyngbya cf. thermalis, Leptolyngbya sp., and Geitlerinema sp.) are also presented. Polyphasic studies that include the combination of light microscopy, cultures and the comparative analysis of 16S rRNA gene sequences provide the most powerful approach currently available to establish the diversity of these oxygenic photosynthetic microorganisms in culture and in nature. Electronic Publication     

Mitochondrial diversity within modern human populations

With the recent increase in the available number of high-quality, full-length mitochondrial sequences, it is now possible to construct and analyze a comprehensive human mitochondrial consensus sequence. Using a data set of 827 carefully selected sequences, it is shown that modern humans contain extremely low levels of divergence from the mitochondrial consensus sequence, differing by a mere 21.6nt sites on average. Fully 84.1% of the mitochondrial genome was found to be invariant and ‘private’ mutations accounted for 43.8% of the variable sites. Ninety eight percent of the variant sites had a primary nucleotide with an allele frequency of 0.90 or greater. Interestingly, the few truly ambiguous nucleotide sites could all be reliably assigned to either a purine or pyrimidine ancestral state. A comparison of this consensus sequence to several ancestral sequences derived from phylogenetic studies reveals a great deal of similarity, where, as expected, the most phylogenetically informative nucleotides in the ancestral studies tended to be the most variable nucleotides in the consensus. Allowing for this fact, the consensus approach provides variation data on the positions that do not contribute to phylogenetic reconstructions, and these data provide a baseline for measuring human mitochondrial variation in populations worldwide.     

Patterns of ecological diversity in fossil and modern mammalian faunas

Ecological diversity provides a means of analysing the community structure of fossil mammalian faunas in order to obtain information on the habitat of the fauna. As a basis for the analysis, 23 modern mammalian communities from distinct habitats have been used to establish patterns of community structure for tropical African habitats according to their species diversity by taxonomic group, size, locomotor zonal adaptation, and feeding adaptation. All the communities tested were in tropical Africa, but additional analyses on tropical forest communities in Australia, Malaya, and Panama have shown that these communities, which all have completely different species composition, nevertheless have community structures very similar to each other and to those of the African forest communities.     

Cyanobacterial ClpC/HSP100 protein displays intrinsic chaperone activity

HSP100 proteins are molecular chaperones that belong to the broader family of AAA+ proteins (ATPases associated with a variety of cellular activities) known to promote protein unfolding, disassembly of protein complexes and translocation of proteins across membranes. The ClpC form of HSP100 is an essential, highly conserved, constitutively expressed protein in cyanobacteria and plant chloroplasts, and yet little is known regarding its specific activity as a molecular chaperone. To address this point, ClpC from the cyanobacterium Synechococcus elongatus (SyClpC) was purified using an Escherichia coli-based overexpression system. Recombinant SyClpC showed basal ATPase activity, similar to that of other types of HSP100 protein in non-photosynthetic organisms but different to ClpC in Bacillus subtilis. SyClpC also displayed distinct intrinsic chaperone activity in vitro, first by preventing aggregation of unfolded polypeptides and second by resolubilizing and refolding aggregated proteins into their native structures. The refolding activity of SyClpC was enhanced 3-fold in the presence of the B. subtilis ClpC adaptor protein MecA. Overall, the distinctive ClpC protein in photosynthetic organisms indeed functions as an independent molecular chaperone, and it is so far unique among HSP100 proteins in having both "holding" and disaggregase chaperone activities without the need of other chaperones or adaptor proteins.     

Cyanobacterial dominance in lakes

Cyanobacterial dominance in lakes has received much attention in the past because of frequent bloom formation in lakes of higher trophic levels. In this paper, underlying mechanisms of cyanobacterial dominance are analyzed and discussed using both original and literature data from various shallow mixed and deep stratifying lakes from temperate and (sub)tropical regions. Examples include all four ecotypes of cyanobacteria sensu Mur et al. (1993), because their behavior in the water column is entirely different. Colony forming species (Microcystis) are exemplified from the large shallow Tai Hu, China. Data from a shallow urban lake, Alte Donau in Austria are used to characterize well mixed species (Cylindrospermopsis), while stratifying species (Planktothrix) are analyzed from the deep alpine lake Mondsee. Nitrogen fixing species (Aphanizomenon) are typified from a shallow river-run lake in Germany. Factors causing the dominance of one or the other group are often difficult to reveal because several interacting factors are usually involved which are not necessarily the same in different environments. Strategies for restoration, therefore, depend on both the cyanobacterial species involved and the specific causing situation. Some uncertainty about the success of correctives, however, will remain due to the stochastic nature of the events and pathways leading to cyanobacterial blooms. Truly integrated research programs are required to generate predictive models capable of quantifying key variables at appropriate spatial and temporal scales.