Morphological complexity affects the diversity of marine microbiomes

Large eukaryotes support diverse communities of microbes on their surface—epibiota—that profoundly influence their biology. Alternate factors known to structure complex patterns of microbial diversity—host evolutionary history and ecology, environmental conditions and stochasticity—do not act independently and it is challenging to disentangle their relative effects. Here, we surveyed the epibiota from 38 sympatric seaweed species that span diverse clades and have convergent morphology, which strongly influences seaweed ecology. Host identity explains most of the variation in epibiont communities and deeper host phylogenetic relationships (e.g., genus level) explain a small but significant portion of epibiont community variation. Strikingly, epibiota community composition is significantly influenced by host morphology and epibiota richness increases with morphological complexity of the seaweed host. This effect is robust after controlling for phylogenetic non-independence and is strongest for crustose seaweeds. We experimentally validated the effect of host morphology by quantifying bacterial community assembly on latex sheets cut to resemble three seaweed morphologies. The patterns match those observed in our field survey. Thus, biodiversity increases with habitat complexity in host-associated microbial communities, mirroring patterns observed in animal communities. We suggest that host morphology and structural complexity are underexplored mechanisms structuring microbial communities.Subject terms: Microbial ecology, Biodiversity     

The ecophysiology of some marine nematodes from Bermuda: Seasonal aspects

In the winter of 1976 the horizontal and vertical distribution, temperature tolerance and oxygen consumption at three experimental temperatures were determined for several species of nematodes inhabiting a low-energy beach in Bermuda. The results are compared with those of previous summer investigations carried out on the same beach.The three most abundant species of nematodes on the beach, Steineria sterreri Ott, Trefusia schiemeri Ott and Theristus floridanus Wieser & Hopper show distinct patterns of distribution as well as distinct survival-time curves when upper lethal temperature is plotted against exposure time. No seasonal resistance adaptation to high temperature occurs in Steineria sterreri and Trefusia schiemeri, the two species for which comparative summer data are available.Theristus erectus, which dominated the flat in summer, is much more heat tolerant than T. Floridanus which replaced it in winter. Oxygen consumption at 15°C is twice as high in T. Floridanus as in Trefusia schiemeri whereas at 22° and 30°C both species consume approximately the same amount of oxygen. T. Schiemeri is capable of seasonal adaptation of Q_O2 inasmuch as it consumes just about as much oxygen in winter at 22°C as in summer at 30°C.The seasonal data support the suggestion that on a subtropical low-energy beach the metabolic capacities of many meiofauna species are closely adjusted to the micro-environment in which they live.     

Phototrophic pigment production with microalgae: biological constraints and opportunities

There is increasing interest in naturally produced colorants, and microalgae represent a bio‐technologically interesting source due to their wide range of colored pigments, including chlorophylls (green), carotenoids (red, orange and yellow), and phycobiliproteins (red and blue). However, the concentration of these pigments, under optimal growth conditions, is often too low to make microalgal‐based pigment production economically feasible. In some Chlorophyta (green algae), specific process conditions such as oversaturating light intensities or a high salt concentration induce the overproduction of secondary carotenoids (β‐carotene in Dunaliella salina (Dunal) Teodoresco and astaxanthin in Haematococcus pluvialis (Flotow)). Overproduction of all other pigments (including lutein, fucoxanthin, and phycocyanin) requires modification in gene expression or enzyme activity, most likely combined with the creation of storage space outside of the photosystems. The success of such modification strategies depends on an adequate understanding of the metabolic pathways and the functional roles of all the pigments involved. In this review, the distribution of commercially interesting pigments across the most common microalgal groups, the roles of these pigments in vivo and their biosynthesis routes are reviewed, and constraints and opportunities for overproduction of both primary and secondary pigments are presented.     

Recent advances in understanding the ecophysiology of enhanced biological phosphorus removal

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Spatio-structural granularity of biological material entities

Background  

With the continuously increasing demands on knowledge- and data-management that databases have to meet, ontologies and the theories of granularity they use become more and more important. Unfortunately, currently used theories and schemes of granularity unnecessarily limit the performance of ontologies due to two shortcomings: (i) they do not allow the integration of multiple granularity perspectives into one granularity framework; (ii) they are not applicable to cumulative-constitutively organized material entities, which cover most of the biomedical material entities.     

The distribution of benthic marine algae

Hitherto only gametangial and carposporangial phases of Thuretellopsis peggiana Kylin have been reported. A study of this rare member of the Dumontiaceae (Cryptonemiales) in culture has disclosed the existence of an encrusting tetrasporangial phase, previously unknown, whilst the life history has been shown to be of the ‘Bonnemaisonia’ type.     

Arctic biogeography: The paradox of the marine benthic fauna and flora

The marine benthic fauna and flora that inhabit the shallow arctic sublittoral zone comprise a relatively young marine assemblage characterized by species of either Pacific or Atlantic affinity and notably few endemics. The young character of nearshore arctic communities, as well as their biogeographical composition, is largely a product of the Pleistocene glaciation. However, analysis of more recent collections and comparison between the origins of the benthic fauna and flora present some interesting paradoxes to biogeographers. One enigma is the low frequency of algal species with Pacific affinities in the Arctic, especially in the Chukchi, Beaufort and East Siberian Seas of the Eastern Arctic, which receive direct inputs of northward-flowing Pacific waters. In contrast, animal species with Pacific affinities are found throughout the nearshore regions of the Arctic, reaching their highest frequency in the marginal seas between the New Siberian Islands and the Canadian Archipelago. Organization of published and unpublished data, additional field collections, and the use of cladistics and molecular DNA techniques by systematists are a high priority for future research in reconstructing the evolution of the arctic biotic assemblage.     

On the origin of Antarctic marine benthic community structure

Environmental conditions fostering marine communities around Antarctica differ fundamentally from those in the rest of the world's oceans, particularly in terms of pronounced climatic fluctuations and extreme cold. Here, we argue that the rarity of pelagic larval stages in Antarctic marine benthic invertebrate species is a consequence of evolutionary temperature adaptation and that this has greatly contributed to the current structure of the Antarctic benthic community. In arguing this position, we challenge the likelihood of previously suggested survival strategies of benthic communities on the Antarctic continental shelf and slope during Cenozoic glacial periods. By integrating evidence from marine geology and geophysics, we suggest that the Antarctic continental shelf and slope were both unfavourable environments for benthic communities during glacial periods and that community survival was only possible in the deep sea or in shelters on the continental shelf as a result of the diachronism in maximum ice extent.     

Matching molecular diversity and ecophysiology of benthic cyanobacteria and diatoms in communities along a salinity gradient

The phylogenetic diversity of oxygenic phototrophic microorganisms in hypersaline microbial mats and their distribution along a salinity gradient were investigated and compared with the halotolerances of closely related cultivated strains. Segments of 16S rRNA genes from cyanobacteria and diatom plastids were retrieved from mat samples by DNA extraction and polymerase chain reaction (PCR), and subsequently analysed by denaturing gradient gel electrophoresis (DGGE). Sequence analyses of DNA from individual DGGE bands suggested that the majority of these organisms was related to cultivated strains at levels that had previously been demonstrated to correlate with characteristic salinity responses. Proportional abundances of amplified 16S rRNA gene segments from phylogenetic groupings of cyanobacteria and diatoms were estimated by image analysis of DGGE gels and were generally found to correspond to abundances of the respective morphotypes determined by microscopic analyses. The results indicated that diatoms accounted for low proportions of cells throughout, that the cyanobacterium Microcoleus chthonoplastes and close relatives dominated the communities up to a salinity of 11% and that, at a salinity of 14%, the most abundant cyanobacteria were related to highly halotolerant cultivated cyanobacteria, such as the recently established phylogenetic clusters of Euhalothece and Halospirulina . Although these organisms in cultures had previously demonstrated their ability to grow with close to optimal rates over a wide range of salinities, their occurrence in the field was restricted to the highest salinities investigated.     

海洋沉积物中重金属对底栖无脊椎动物的生物有效性

海洋沉积物是重金属的重要贮库,而海洋底栖无脊椎动物主要从沉积物中摄取重金属,这些被摄取的重金属能够通过食物链进行传递,进而影响到人类健康。本文总结了近些年来在海洋沉积物中重金属对底栖无脊椎动物生物有效性方面的研究进展,包括海洋底栖无脊椎动物对重金属的吸收途径、沉积物地球化学性质和底栖无脊椎动物生理等生物因素对沉积物中重金属生物有效性的影响。在此基础上,展望了未来研究重点,主要包括近海富营养化对沉积物中重金属生物有效性的影响,海洋底栖无脊椎动物消化道中的物理消化过程对沉积物中重金属生物有效性的影响,海洋底栖无脊椎动物整个生活史过程中沉积物中重金属生物有效性的变化等。     

Linking the planktonic and benthic habitat: genetic structure of the marine diatom Skeletonema marinoi

Dormant life stages are important strategies for many aquatic organisms. The formation of resting stages will provide a refuge from unfavourable conditions in the water column, and their successive accumulation in the benthos will constitute a genetic reservoir for future planktonic populations. We have determined the genetic structure of a common bloom‐forming diatom, Skeletonema marinoi, in the sediment and the plankton during spring, summer and autumn two subsequent years (2007–2009) in Gullmar Fjord on the Swedish west coast. Eight polymorphic microsatellite loci were used to assess the level of genetic differentiation and the respective gene diversity of the two different habitats. We also determined the degree of genetic differentiation between the seed banks inside the fjord and the open sea. The results indicate that Gullmar Fjord has one dominant endogenous population of S. marinoi, which is genetically differentiated from the open sea population. The fjord population is encountered in the plankton and in the sediment. Shifts from the dominant population can happen, and in our study, two genetically differentiated plankton populations, displaying reduced genetic diversity, occurred in September 2007 and 2008. Based on our results, we suggest that sill fjords maintain local long‐lived and well‐adapted protist populations, which continuously shift between the planktonic and benthic habitats. Intermittently, short‐lived and mainly asexually reproducing populations can replace the dominant population in the water column, without influencing the genetic structure of the benthic seed bank.     

Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine sponges

The biosynthesis of non-ribosomal peptide and polyketide natural products is facilitated by multimodular enzymes that contain domains responsible for the sequential condensation of amino and carboxylic subunits. These conserved domains provide molecular targets for the discovery of natural products from microbial metagenomes. This study demonstrates the application of tag-encoded FLX amplicon pyrosequencing (TEFAP) targeting non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) genes as a method for determining the identity and diversity of natural product biosynthesis genes. To validate this approach, we assessed the diversity of NRPS and PKS genes within the microbiomes of six Australian marine sponge species using both TEFAP and metagenomic whole-genome shotgun sequencing approaches. The TEFAP approach identified 100 novel ketosynthase (KS) domain sequences and 400 novel condensation domain sequences within the microbiomes of the six sponges. The diversity of KS domains within the microbiome of a single sponge species Scopalina sp. exceeded that of any previously surveyed marine sponge. Furthermore, this study represented the first to target the condensation domain from NRPS biosynthesis and resulted in the identification of a novel condensation domain lineage. This study highlights the untapped potential of Australian marine sponges for the isolation of novel bioactive natural products. Furthermore, this study demonstrates that TEFAP approaches can be applied to functional genes, involved in natural product biosynthesis, as a tool to aid natural product discovery. It is envisaged that this approach will be used across multiple environments, offering an insight into the biological processes that influence the production of secondary metabolites.     

Appearance and evolution of marine benthic communities in the Early Palaeozoic

The development of marine benthic communities in the Early Palaeozoic occurred mainly in the shallow water epicontinental seas. It included those stages of the Cambrian and Ordovician evolutionary radiations that were dominated by a high rate of morphogenesis, when new food and territory resources were not limited. This provided many opportunities for coadaptation of emerging organisms. At the time of the Cambrian radiation, the body plans of all animals were formed, while in the Ordovician, the maximum rank of emerging taxa did not exceed the level of class. The beginning of each radiation was explosive. Vendian benthic communities developed in cold seas and in the shallowest areas of warm seas, where organic matter from the surface layers was available at the bottom because of the absence of a thermocline. The Cambrian radiation began with the appearance of pelagic suspension feeders, because of which much of the primary production could penetrate the thermocline and settle at the bottom. This allowed the occupation of warmer seas and greater depths. At the same time, the productivity of the pelagic region sharply increased because of the emergence of positive feedback between the producers and consumers in the water, leading to increased water transparency and elongation of trophic chains. Arthropods, the first suspension feeders, were the launch group of the Cambrian radiation. Cambrian benthic suspension feeders could seize only the smallest particles, mostly bacteria, and dissolved organic matter. This food resource was contained in the thin bottom water layer. Therefore, the food grasping structures of all the Cambrian suspension feeders were near the bottom, without forming tiers. The Ordovician evolutionary radiation began with the launch of the Pelmatozoan echinoderms, which were the first benthic suspension feeders to begin feeding on plankton. The exploitation of this resource led to the creation of a 1-m tier above the bottom and an increase in their calcite productivity. Positive feedback emerged between the grounds and the community of its inhabitants and considerably changed the composition and diversity of grounds, which sharply increased the diversity of benthos. The appearance of positive feedback between different components of ecosystems resulted in explosive evolution in both the Cambrian and Ordovician.     

Physical properties of biological entities: an introduction to the ontology of physics for biology

As biomedical investigators strive to integrate data and analyses across spatiotemporal scales and biomedical domains, they have recognized the benefits of formalizing languages and terminologies via computational ontologies. Although ontologies for biological entities-molecules, cells, organs-are well-established, there are no principled ontologies of physical properties-energies, volumes, flow rates-of those entities. In this paper, we introduce the Ontology of Physics for Biology (OPB), a reference ontology of classical physics designed for annotating biophysical content of growing repositories of biomedical datasets and analytical models. The OPB's semantic framework, traceable to James Clerk Maxwell, encompasses modern theories of system dynamics and thermodynamics, and is implemented as a computational ontology that references available upper ontologies. In this paper we focus on the OPB classes that are designed for annotating physical properties encoded in biomedical datasets and computational models, and we discuss how the OPB framework will facilitate biomedical knowledge integration.     

Alkali-labile precursors of dimethyl sulfide in marine benthic cyanobacteria

By the method of cold alkali hydrolysis, 29 marine benthic cyanobacteria were screened for production of alkali-labile precursors of dimethyl sulfide (DMS) including dimethylsulfoniopropionate (DMSP), a compound of significant importance in marine environments. Concentrations of DMS precursors ranged from undetectable to 0.8 mmol (g Chl a)^–1. The data correspond to some previous investigations concerning DMSP content of marine cyanobacteria and suggest that marine benthic cyanobacteria are only minor producers of DMSP. Received: 3 July 1997 / Accepted: 21 October 1997     

洞穴微生物组:已知与未知

洞穴是由于岩石受到溶蚀或火山岩浆冷却形成的地下空间和通道。洞穴遍布世界各地,蕴藏着大量的微生物资源。洞穴内黑暗潮湿,温度相对稳定,营养比较贫瘠,是一种极端的生态系统,存在着高度特异性的洞穴微生物。对洞穴微生物组的研究,有助于认知洞穴微生物群体结构、组成及其地理学分布,加深对洞穴生态系统的理解,并为保护和开发洞穴资源提供指导。本文主要介绍了洞穴微生物组的研究方法,总结分析了洞穴微生物的研究进展,并着重阐述了含特殊化合物成分的洞穴中化能自养的特色微生物组。     

Late Devonian benthic marine communities of the central Appalachian Allegheny Front

Four benthic marine communities occur in the clastic facies of the prograding Upper Frasnian-Lower Famennian (Upper Devonian) Foreknobs Formation in the Central Appalachians along the Allegheny Front in Maryland, West Virginia, and Virginia. Deep-water, rapidly prograding environments were inhabited by the Ambocoelia-Chonetes Community, dominated by an epifauna of unattached brachiopods. Offshore bar environments were inhabited by the Cyrtospirifer-Camarotoechia Community, exhibiting adaptations to shallow-water, high-energy conditions and probably lowered salinities. Shallow-water, sublittoral environments were inhabited by the Atrypa-Cypricardella Community, a community in which existed a variety of life habitats and a diverse epifaunal and infaunal association of brachiopods and bivalve molluscs. The Leptodesma-Tylothyris Community flourished in nearshore bar-protected environments in the southern region of the study area, whereas in the north the Cyrtospirifer-Camarotoechia Community inhabited nearshore environments in conjunction with the onshore development of a large fluviodeltaic system.     

Phosphatase activity of benthic marine algae. An overview

This review provides an account of the phosphatase activities of benthicmarine algae and is based on reports for more than a hundred species, includingcyanobacteria, red, brown and green algae. Particular emphasis is given to theuse of phosphomonoesterase activity as a rapid means of assessing thephosphorusstatus of the alga and thus indirectly that of the environment. Anunderstandingof the influence of environmental factors and the growth pattern of theparticular alga is important in carrying out assays. For instance, the responseto light differs markedly between species, especially in short-term assays,whenthe effect can be obvious or none. Considerations about the methodology formeasuring "alkaline phosphatase activity" are discussed, particularly whethertosimulate field conditions or to use optimum conditions. Recommendations aresuggested concerning the best methodology for routine use, followed by adiscussion of the future prospects for the method.