Threatened corals provide underexplored microbial habitats

Contemporary in-depth sequencing of environmental samples has provided novel insights into microbial community structures, revealing that their diversity had been previously underestimated. Communities in marine environments are commonly composed of a few dominant taxa and a high number of taxonomically diverse, low-abundance organisms. However, studying the roles and genomic information of these “rare” organisms remains challenging, because little is known about their ecological niches and the environmental conditions to which they respond. Given the current threat to coral reef ecosystems, we investigated the potential of corals to provide highly specialized habitats for bacterial taxa including those that are rarely detected or absent in surrounding reef waters. The analysis of more than 350,000 small subunit ribosomal RNA (16S rRNA) sequence tags and almost 2,000 nearly full-length 16S rRNA gene sequences revealed that rare seawater biosphere members are highly abundant or even dominant in diverse Caribbean corals. Closely related corals (in the same genus/family) harbored similar bacterial communities. At higher taxonomic levels, however, the similarities of these communities did not correlate with the phylogenetic relationships among corals, opening novel questions about the evolutionary stability of coral-microbial associations. Large proportions of OTUs (28.7–49.1%) were unique to the coral species of origin. Analysis of the most dominant ribotypes suggests that many uncovered bacterial taxa exist in coral habitats and await future exploration. Our results indicate that coral species, and by extension other animal hosts, act as specialized habitats of otherwise rare microbes in marine ecosystems. Here, deep sequencing provided insights into coral microbiota at an unparalleled resolution and revealed that corals harbor many bacterial taxa previously not known. Given that two of the coral species investigated are listed as threatened under the U.S. Endangered Species Act, our results add an important microbial diversity-based perspective to the significance of conserving coral reefs.

The diversity and ecological role of protozoa in fresh waters

Protozoa feed on and regulate the abundance of most types of aquatic microorganisms, and they are an integral part of all aquatic microbial food webs. Being so small, aerobic protozoa thrive at low oxygen tensions, where they feed (largely unaffected by metazoan grazing) on the abundance of other microorganisms. In anaerobic environments, they are the only phagotrophic organisms, and they live in unique symbiotic consortia with methanogens, sulphate reducers and non-sulphur purple bacteria. The number of extant species of protozoa may be quite modest (the global number of ciliate species is estimated at 3000), and most of them probably have cosmopolitan distributions. This will undoubtedly make it easier to carry out further tasks, e.g. understanding the role of protozoan species diversity in the natural environment.

Does Long-Term Macrophyte Management in Lakes Affect Biotic Richness and Diversity?

We hypothesize that the richness and diversity of the biota in Lake Moraine (42°50’47”N, 75°31’39”W) in New York have been negatively impacted by 60 years of macrophyte and algae management to control Eurasian watermilfoil ( Myriophyllum spicatum L.) and associated noxious plants. To test this hypothesis we compare water quality characteristics, richness and selected indicators of plant diversity, zooplankton, benthic macroinvertebrates and fish in Lake Moraine with those in nearby Hatch Lake (42°50’06”N, 75°40’67”W). The latter is of similar size and would be expected to have similar biota, but has not been subjected to management. Measurements of temperature, pH, oxygen, conductivity, Secchi transparency, calcium, total phosphorus and nitrites + nitrates are comparable. Taxa richness and the diversity indices applied to the aquatic macrophytes are similar in both lakes. (PDF has 8 pages.)

Comparative Microbial Dynamics in Crassostrea virginica and Crassostrea ariakensis

Considerations to introduce the Suminoe or Asian oyster Crassostrea ariakensis along the East Coast have raised many questions regarding ecology, economics, and human health. To date, research has focused primarily on the ecological and socioeconomic implications of this initiative, yet few studies have assessed its potential impact on public health. Our work compares the rates of bioaccumulation, depuration and post harvest decay of indicator organisms (such as E. coli) and Vibrio sp. between Crassostrea virginica and Crassostrea ariakensis in the laboratory. Preliminary results suggest that the rates of bioaccumulation of E. coli in Crassostrea ariakensis were significantly lower than those for Crassostrea virginica, depuration of E. coli was variable between the two species, and Crassostrea ariakensis post harvest decay rates of Vibrio sp. were significantly lower than Crassostrea virginica. This research provides coastal managers with insight into the response of Crassostrea ariakensis to bacteria, an important consideration for determining appropriate management strategies for this species. Further field-based studies will be necessary to elucidate the mechanisms responsible for the differences in rates of bioaccumulation and depuration. (PDF contains 40 pages)

Structure and diversity in Mytilus californianus (Mollusca: Bivalvia) communities

Mytilus californianus (Mollusca: Bivalvia), the California marine mussel, occurs in intertidal populations so derise that they are referred to as "Mussel beds." The mussel beds range in physical complexity from structurally simple, essentially mono-layered assemblages, to structurally complex, multi-layered assemblages. The internal environment within the bed varies accordingly. The mussel bed provides either directly or indirectly, habitat, food and shelter for a large community of associated invertebrates. This study examines the relationship between physical complexity of the mussel bed habitat and composition of the associated community.

Fish diversity of the wild and aquaculture water bodies in Singida Region

Tanzania Fisheries Research Institute being currently the only fisheries research institute in Tanzania has sole responsibility of marking the presence and distribution of fish species in the country. This work is expected to be completed by the year 2005. In order that this work can be accomplished, both published works and field observations (including geographical location using GPS) have to be compiled. Since the institute has centers in all the Great Lakes and one along the Indian Ocean coast, it is expected that field observations and identifications will be obtained and incorporated into the document to be produced by 2005. (PDF contains 15 pages)

The importance of periodic droughts for maintaining diversity in the freshwater environment

Whereas some species may rely on periodic drought conditions for part of their life histories, or have life strategies suited to exploiting the habitat or changed environmental conditions that are created by drought, for other organisms it is a time of stress. Periodic drought conditions therefore generate a series of waves of colonization and extinctions. Studies on lowland wet grassland, in winterbournes and in the toiche zone of both ponds and rivers, also demonstrate that different organisms are competitively favoured with changing hydrological conditions, and that this process prevents any one species from overwhelming its competitors. Competitive impacts may be inter- and intraspecific. It is therefore apparent that the death of organisms such as adult fish during severe drought conditions, though traumatic for human onlookers and commercial interests, may be merely a regular occurrence to which the ecosystem is adapted. The variability of climatic conditions thereby provides a direct influence on the maintenance of biological diversity, and it is this very biodiversity that provides the ecosystem with the resilience to respond to environmental changes in both the short and the longer term.

Environmental variables and fisheries diversity of the Naaf River Estuary, Bangladesh

The Naaf River estuary is one of the large estuaries in the Bangladesh coastal region not to have been affected by extensive human disturbance. This research provides information about the fisheries diversity status by Estuarine Set Bag Net (ESBN) sampling relation to physicochemical variables in both spatio-temporal scales. About 25 km of the lower estuary was divided into six zones for sample collection by considering the accessibility and availability of the ESBN operation, fish landing centers and location of the fishing villages. In total 48 samples have been analyzed which were taken throughout March to October 2006. To quantify the species diversity, all fisheries data were analyzed by using EstimateS and EcoSim software which accounts the different diversity indices viz., species richness, Shannon–Wiener diversity Index, Dominance and Evenness index. The research results demonstrate that the Naaf River estuary is a habitat of 161 (species richness, Sobs=161, Choa 1=162±2.34, ACE=161.73) different species which belong to 98 fin fishes, 23 shrimps and prawns,13 crabs, 11 molluscs, 3 echinoderms, 4 other crustaceans;while 9 remain unidentified. Results on the aquatic environment,mainly salinity and turbidity were found to have a major influence on their occurrence and distribution. All the findings indicated that the Naaf River estuary is a highly productive system and provides a favourable environment for large variety of estuarine species assemblages.

The microbiological quality of water: the nature of the problem

Improvements in methods for the detection and enumeration of microbes in water, particularly the application of techniques of molecular biology, have highlighted shortcomings in the ”standard methods” for assessing water quality. Higher expectations from the consumer and increased publicity associated with pollution incidents can lead to an uncoupling of the cycle which links methodological development with standard-setting and legislation. The new methodology has also highlighted problems within the water cycle, related to the introduction, growth and metabolism of microbes. A greater understanding of the true diversity of the microbial community and the ability to transmit genetic information within aquatic systems ensures that the subject of this symposium and volume provides an ideal forum to discuss the problems encountered by both researcher and practitioner.

The impact of molecular biology on assessment of water quality: advantages and limitations of current techniques

The advent of molecular biology has had a dramatic impact on all aspects of biology, not least applied microbial ecology. Microbiological testing of water has traditionally depended largely on culture techniques. Growing understanding that only a small proportion of microbial species are culturable, and that many microorganisms may attain a viable but non-culturable state, has promoted the development of novel approaches to monitoring pathogens in the environment. This has been paralleled by an increased awareness of the surprising genetic diversity of natural microbial populations. By targeting gene sequences that are specific for particular microorganisms, for example genes that encode diagnostic enzymes, or species-specific domains of conserved genes such as 16S ribosomal RNA coding sequences (rrn genes), the problems of culture can be avoided. Technical developments, notably in the area of in vitro amplification of DNA using the polymerase chain reaction (PCR), now permit routine detection and identification of specific microorganisms, even when present in very low numbers. Although the techniques of molecular biology have provided some very powerful tools for environmental microbiology, it should not be forgotten that these have their own drawbacks and biases in sampling. For example, molecular techniques are dependent on efficient lysis and recovery of nucleic acids from both vegetative forms and spores of microbial species that may differ radically when growing in the laboratory compared with the natural environment. Furthermore, PCR amplification can introduce its own bias depending on the nature of the oligonucleotide primers utilised. However, despite these potential caveats, it seems likely that a molecular biological approach, particularly with its potential for automation, will provide the mainstay of diagnostic technology for the foreseeable future.

Effects of trawling for ocean shrimp (Pandalus jordani) on macroinvertebrate abundance and diversity at four sites near Nehalem Bank, Oregon

Surveys with a remotely operated vehicle (ROV) at four mudhabitat sites with different histories of ocean shrimp (Pandalus jordani) trawling showed measurable effects of trawling on macroinvertebrate abundance and diversity. Densities of the sea whip (Halipteris spp., P<0.01), the flat mud star (Luidia foliolata, P< 0.001), unidentified Asteroidea (P<0.05), and squat lobsters (unidentified Galathoidea, P<0.001) were lower at heavily trawled (HT) sites, as was invertebrate diversity based on the Shannon-Wiener index. Sea cucumbers (unidentified Holothuroidea) and unidentified corals (Hydrocoralia) were observed at lightly trawled (LT) sites but not at HT sites. Hagfish (Eptatretus spp.) burrows were the dominant structural feature of the sediment surface at all sites and were more abundant at the HT sites (P<0.05), a result potentially related to effects from fishery discards. Substantial heterogeneity was found between the northern and southern site pairs, indicating high site-to-site variability in macroinvertebrate densities in these deep (146–156 m) mud habitats. Two of the study sites were closed to trawling in June 2006. The data from this study can be used in combination with future surveys to measure recovery rates of deep, mud, seaf loor habitats from the effects of trawling, thus providing a critical piece of information for ecosystem-based management.