Real-time PCR assay for detection and relative quantification of <Emphasis Type="Italic">Liocarcinus </Emphasis><Emphasis Type="Italic">depurator</Emphasis> larvae from plankton samples

Accurate species identification of decapod crustacean larvae is required to understand their population distributions, life cycle dynamics and interactions with their habitats. Analysis of plankton samples using morphological taxonomic methods and microscopy is time-consuming, requires highly skilled and trained operatives and may often be inaccurate. As complementary tools to classical identification methods, recent work has focused on the development of molecular approaches and shows their feasibility for species-specific identification. This study has developed real-time PCR assays utilising species-specific Taqman^® probes designed in the cytochrome oxidase I (COI) gene of Liocarcinus depurator, Necora puber, Carcinus maenas and Cancer pagurus. Our study then employed the probe and primers designed for L. depurator to obtain accurate identification and relative abundance estimates of L. depurator larvae in plankton samples collected between March 2005 and October 2006. Ranges of larval abundances were derived from a standard curve created from plankton samples spiked with a known number of larvae reared in the laboratory. Inhibition of the PCR reaction was shown to be an important factor and our results suggested that 0.1 ng of DNA as template provided accurate identification and avoided inhibition. Real-time PCR was shown to provide accurate species identification on unsorted plankton samples and could be suitable for the estimation of larval abundances in the plankton, although more work must be done to improve the accuracy of those estimations.     

Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR)

Quantification of feeding rates and selectivity of zooplankton is vital for understanding the mechanisms structuring marine ecosystems. However, methodological limitations have made many of these studies difficult. Recently, molecular based methods have demonstrated that DNA from prey species can be used to identify zooplankton gut contents, and further, quantitative gut content estimates by quantitative PCR (qPCR) assays targeted to the 18S rRNA gene have been used to estimate feeding rates in appendicularians and copepods. However, while standard single primer based qPCR assays were quantitative for the filter feeding appendicularian Oikopleura dioica, feeding rates were consistently underestimated in the copepod Calanus finmarchicus. In this study, we test the hypothesis that prey DNA is rapidly digested after ingestion by copepods and describe a qPCR-based assay, differential length amplification qPCR (dla-qPCR), to account for DNA digestion. The assay utilizes multiple primer sets that amplify different sized fragments of the prey 18S rRNA gene and, based on the differential amplification of these fragments, the degree of digestion is estimated and corrected for. Application of this approach to C. finmarchicus fed Rhodomonas marina significantly improved quantitative feeding estimates compared to standard qPCR. The development of dla-qPCR represents a significant advancement towards a quantitative method for assessing in situ copepod feeding rates without involving cultivation-based manipulation.     

Single-step species identification of bivalve larvae using multiplex polymerase chain reaction

One of the biggest obstacles to studying recruitment variation in marine bivalves is the need to collect and process large numbers of plankton samples. Larval bivalves are notoriously difficult, if not impossible, to identify to species using morphological criteria alone. Remote time-series collections could satisfy the sampling challenge, but efficient identification techniques must be developed to obtain species-specific data. Thus, we have developed a multiplex polymerase chain reaction (PCR) identification assay in which a single reaction is capable of accurate and efficient discrimination of five target bivalve species based on the size of cytochrome oxidase I products. The assay was tested with cultured and field-sampled larvae as well as adult genomic DNAs. Using a single whole larva as template, multiplex PCR reactions were capable of discriminating among the commercially important bivalves: Mercenaria mercenaria, Argopecten irradians, Mulinia lateralis, Spisula solidissima and Mya arenaria. Overall accuracy was 92%, including very few false positives. The efficiency of this assay stems from its ability to discriminate multiple target species with a single molecular step that ultimately can be automated to process large numbers of larvae. Received: 30 March 2000 / Accepted: 10 July 2000     

环境DNA(eDNA)宏条形码技术对枝角类浮游动物物种鉴定及其生物量监测研究

环境DNA(eDNA)宏条形码(Metabarcoding)技术越来越多地被应用于环境中物种定性识别,但如何定量监测物种在环境中的丰度尚未得到解决。本研究以太湖流域常见的5种浮游动物拟同形溞、大型溞、蚤状溞、多刺裸腹溞、老年低额溞为研究对象,建立了一种基于eDNA宏条形码技术的物种定量方法,并与实时荧光定量PCR(qPCR)相比较,研究了eDNA宏条形码技术多物种定量的准确性。结果表明,PCR引物对eDNA宏条形码的物种检测和定量影响显著。313 bp COI313引物对浮游动物物种覆盖度高,但是物种间DNA扩增的偏好性大,不适用于eDNA宏条形码定量检测。基于COI序列重新设计的短COI116引物能够同时检测出所有5个物种。荧光定量PCR(qPCR)物种拷贝数与物种相对占比呈正相关。eDNA宏条形码所检出每个物种的序列数与qPCR定量拷贝数高度一致。综上,eDNA宏条形码技术可实现对浮游动物物种的半定量检测,在生物多样性监测和生物完整性评价有显著的应用价值。     

Identification of bivalve species at an early developmental stage through PCR-SSCP and sequence analysis of partial 18S rDNA

The notorious difficulties encountered in species identification of bivalve larvae through morphological characters have given rise to several alternative molecular approaches. In the present work, we propose a method based on PCR-SSCP combined with sequencing of partial 18S rDNA region, in which a large number of larvae can be scored and species identified with minimum sequencing effort. A primer set was developed to amplify a taxonomically informative 18S region of fragment size suitable for high resolution PCR-SSCP. The method developed is fast processing and has the potential of identifying most species present in a plankton sample with low economic efforts. Those species for which partial 18S sequences are not yet available from GenBank, can be identified in families or at higher categories. The method was also tested on nine species and two subspecies of commercial importance in Italy to be carried out by the use of PCR-SSCP alone without sequencing.     

林木外生菌根真菌彩色豆马勃巢式PCR检测

为探讨林木外生菌根真菌的分子检测方法,利用真菌通用引物ITS1-F/ITS4-B扩增了外生菌根真菌彩色豆马勃的核糖体DNA内转录间隔区并进行了序列测定.通过序列比较,设计了一对彩色豆马勃特异性引物PtF/PtR.利用该对特异性引物与ITS1-F/ITS4-B组合进行巢式PCR,能从供试的彩色豆马勃10个菌株中特异性地扩增出1条347 bp的条带,而供试的其他6个参比菌株未出现扩增产物.经分析,该巢式PCR检测技术的灵敏度可达到10 fg的DNA,是常规PCR检测的1 000倍.利用该技术从马尾松苗木菌根中检测到目的外生菌根真菌.这表明采用本研究设计的特异性引物,利用巢式PCR技术可以灵敏、准确地从林木外生菌根中检测出彩色豆马勃.     

浮游动物DNA宏条形码标志基因比较研究

DNA宏条形码技术作为一种新型生物监测方法,在未来生态环境监测中有巨大的应用潜力。目前,浮游动物DNA宏条形码监测仍在发展阶段,需要首先对其(采样方法、引物选择和数据分析等)进行标准化和调整,然后才能用于常规流域生态监测。其中,如何选择合适的PCR扩增引物是DNA宏条形码生物监测标准化的关键问题之一。本研究比较了COI、18SV9和16S通用引物在浮游动物DNA宏条形码监测中的差异,为初步建立规范化的浮游动物DNA宏条形码监测方法提供技术支撑。结果表明,16S引物对浮游动物具有更好的特异性,其产生的操作分类单元(operational taxonomic unit, OTU)有88.1%属于浮游动物。虽然18SV9引物具有更高的物种覆盖度,不仅能扩增出浮游动物,还能扩增出大量藻类和真菌,但其物种识别敏感性较差,不适合浮游动物物种水平多样性监测。COI引物的浮游动物物种特异性、物种覆盖度和物种识别敏感性都适中,检出的浮游动物物种数量高于18SV9引物和16S引物,更加适合浮游动物DNA宏条形码监测。     

Apparent predation on ichthyoplankton by zooplankton and fishes in nearshore waters of southern California

Plankton collected at discrete depths in Santa Monica Bay, California, USA, during January 1982 were examined for fish eggs and larvae that had been attacked or consumed by zooplankton. The bongo net remained open for only 3 min and samples were preserved within 5 min of capture. Juvenile and adult fishes that had been captured by otter trawl and preserved within 20 min of capture were examined for ingested fish eggs and larvae. Three copepods (Corycaeus anglicus, Labidocera trispinosa, and Tortanus discaudatus), one euphausid larva (Nyctiphanes simplex), one amphipod (Monoculoides sp.), and an unidentified decapod larva were found attached to fish larvae in the preserved plankton samples (attachment to 23% of the fish larvae was observed in one sample). Overall, about 5% of the white croaker (Genyonemus lineatus) larvae and 2% of the northern anchovy (Engraulis mordax) larvae had attached zooplankton predators. Most fish larvae with attached zooplankton predators were small. We found no indication of zooplankton predation on fish eggs. Few fish eggs and larvae were found in the digestive tracts of juvenile or adult fishes, and the ingested fish larvae were relatively large. The discussion considers apparent preyspecificity of the zooplankton predators as well as potential biases that may be associated with preserved samples collected by nets.     

Quantitative PCR to estimate copepod feeding

Copepods play a central role in marine food webs as grazers of plankton and as key prey for many predators. Therefore, quantifying their specific trophic interactions is critical for understanding the role of copepods in ocean processes. However, because of methodological constraints, it remains difficult to investigate in situ copepod feeding without reliance on laborious intrusive and potentially biased incubation approaches. Recent advances in PCR-based methodologies have demonstrated the feasibility of directly identifying copepod diets based on prey DNA sequences. Yet, obtaining quantitative information from these approaches remains challenging. This study presents results of systematic efforts to develop a quantitative PCR (qPCR) assay targeted to 18S rRNA gene fragments to estimate copepod gut content of specific species of prey algae. These results were first compared to gut content estimates based on fluorescence in the copepod Calanus finmarchicus fed monocultures of two different microalgae species in controlled laboratory studies. In subsequent field studies, we compared feeding rates obtained by microscopy and qPCR for Temora longicornis and Acartia clausi feeding on the haptophyte Phaeocystis globosa in natural blooms. These investigations demonstrate a semi-quantitative relationship between gut content estimates derived from qPCR, gut pigment, and direct microscopy. However, absolute estimates of gut content based on qPCR methodology were consistently lower than expected. This did not appear to be explained by the extraction methods used, or interference by non-target (predator) DNA in the PCR reactions, instead suggesting digestion of prey-specific nucleic acids. Furthermore, the 18S rDNA target gene copy number of the phytoplankton varied with growth phase. Nonetheless, when prey target gene copy number in the ambient water is quantified, the qPCR-approach can be compared to other methods, and then used to semi-quantitatively estimate relative copepod grazing on specific prey in situ without involving further incubations. A distinct advantage of a DNA-based molecular approach compared to gut fluorescence and direct microscopic observation, is the ability to detect non-pigmented and macerated prey. Future studies should aim to correct for breakdown in prey DNA and perform extensive calibrations to other methods in order to achieve a quantitative measure of feeding rates in situ.     

Differential ingestion of zooplankton by four species of bivalves (Mollusca) in the Mali Ston Bay,Croatia

This study provides information about differences in composition of ingested zooplankton amongst bivalve species coexisting in the same area in a period from May 2009 to December 2010. The study was conducted at the Mali Ston Bay (42°51′ N, 17°40′ E)—the most important bivalve aquaculture area in the eastern Adriatic Sea. Stomach content analysis was performed on cultured species—Ostrea edulis and Mytilus galloprovincialis, and commercially important bivalve species from their natural environment—Modiolus barbatus and Arca noae. Results confirmed carnivory in bivalves, both from natural and cultured populations, but cultured species had higher numbers of zooplankters than those living on the seabed. The most abundant taxa were bivalve larvae, followed by tintinnids, copepods, unidentified eggs and gastropod larvae. Recorded numbers of bivalve larvae in M. galloprovincialis stomach were the highest so far reported and show that mussels impact the availability of natural spat.     

A molecular approach for the identification of meiofaunal turbellarians (Platyhelminthes,Turbellaria)

In the absence of reliable morphological characters, or in conjunction with morphology-based identifications, meiofaunal turbellarians may also be identified using the nucleotide sequence of a portion of the large subunit of the ribosomal RNA (26/28S rRNA). A 284 base pair-long region of the 26/28S rRNA has been identified by isolating genomic DNA from ten species of turbellarians belonging to four orders, namely, the Proseriata, Macrostomida, Prolecithophora and Acoela. The proseriates had been collected from localities in Europe and Israel and were preserved in ethanol. The remaining turbellarians were isolated from intertidal sediment samples collected from two sites on the Maine and New Hampshire coast, USA in 1992. Amplification of the genomic DNA was carried out using two primers designed to match the nucleotide sequence of a portion of the 26/28S rDNA gene of the terrestrial nematode,Caenorhabditis elegans (Maupas 1900). This area consists of a highly variable, about 150 base pair-long region, called the D3 expansion segment, followed by a very conserved stretch of sequence. When folded into its secondary structure, the conserved region will form stem structures that correspond to helices 15 to 18 of theC. elegans structural model. The sequence alignment program PILEUP was used to perform a cluster analysis (unweighted pair group method using arthmetic averages, UPGMA) on the sequences. This analysis revealed that the helices allow for the classification of the turbellarians at the level of families and above, whereas if the D3 expansion segment itself was included in the analysis, intrageneric and intraspecific groupings could be established.     

Evidence for a symbiosis between bacteria of the genus Rhodobacter and the marine sponge Halichondria panicea : harbor also for putatively toxic bacteria?

Halichondria panicea (Pallas) is a marine sponge, abundantly occurring in the Adriatic Sea, North Sea, and Baltic Sea. It was the aim of the present study to investigate if this sponge species harbors bacteria. Cross sections through H. panicea were taken and inspected by electron microscopy. The micrographs showed that this sponge species is colonized by bacteria in its mesohyl compartment. To identify the bacteria, polymerase chain reaction (PCR) analysis of the 16S rRNA gene segment, typical for bacteria, was performed. DNA was isolated from sponge material that had been collected near Rovinj (Adriatic Sea), Helgoland (North Sea), and Kiel (Baltic Sea) and was amplified with bacterial primers by PCR. The data gathered indicate that in all samples bacteria belonging to the genus Rhodobacter (Proteobacteria, subdivision α) are dominant, suggesting that these bacteria live in symbiotic relationship with the sponge. In addition, the results show that the different samples taken contain further bacterial species, some of them belonging to the same genus even though found in sponges from different locations. The possibility of the presence of toxic bacteria was supported by the finding that organic extracts prepared from sponge samples displayed toxicity, when analyzed in vitro using leukemia cells. Received: 7 March 1997 / Accepted: 2 October 1997     

Fine-scale distribution of larval fishes: patterns and processes adjacent to coral reefs in Kaneohe Bay,Hawaii

Plankton samples were taken from January to June 1987 in Kaneohe Bay, Oahu, Hawaiian Islands, with a free-fall plankton net, to investigate the fine-scale distribution of larval fishes around coral reefs. Daytime samples indicated that the postflexion larvae of two gobiids (Psilogobius mainlandi and an unidentified species) were significantly more abundant at stations immediately adjacent to reefs (near-reef) than at stations in open water off the reef (off-reef). These postflexion gobiid larvae appeared to be capable of resisting advection and dispersal while remaining in the water column near suitable adult habitats. The larvae of Foa brachygramma (Apogonidae) and Encrasicholina purpurea (Engraulidae) were significantly more abundant at off-reef stations than at near-reef stations. Nighttime samples indicated that the gobiid larvae depend on visual cues to remain near the reef. The horizontal distributions of F. brachygramma and E. purpurea larvae appeared to be related to their vertical positioning. These data suggest that typical ichthyoplankton surveys which do not sample close to adult fish habitats would greatly underestimate the abundances of larvae such as the gobiids.     

Lethal effects of Northwest Atlantic Ocean isolates of the dinoflagellate, Scrippsiella trochoidea, on Eastern oyster (Crassostrea virginica) and Northern quahog (Mercenaria mercenaria) larvae

The thecate dinoflagellate Scrippsiella trochoidea is a cosmopolitan, bloom-forming alga that has been generally considered non-toxic. Here, we report that environmentally relevant cell densities (10⁴ cells mL⁻¹) of Scrippsiella trochoidea strains isolated from the Northwest Atlantic Ocean caused 100% mortality in Eastern oyster (Crassostrea virginica) larvae during 3-day exposures while parallel control larvae exhibited 100% survival. S. trochoidea also exhibited lethal effects on Northern quahog (Mercenaria mercenaria) larvae (70% mortality during 3-day exposure) but were non-toxic to juvenile fish (Cyprinodon variegates). The cultures of S. trochoidea were more lethal to Northern quahog larvae than ten other species of harmful algae, including the highly toxic species Cochlodinium polykrikoides. Scrippsiella trochoidea cultures within later stages of growth were more toxic than exponential growth stages to bivalve larvae, and the toxicity was dose dependent. Furthermore, toxicity was maintained in the cultures that were sonicated, boiled, and frozen as well as in resuspended residues of the culture but was significantly lower in cell-free culture media. Collectively, these results suggest that S. trochoidea causes mortality in bivalve larvae through a physicochemical rather than strictly chemical mechanism, such as clogging of larval feeding apparatuses by materials produced by S. trochoidea (e.g., lipids, extracellular polysaccharides, and/or cell debris) which accumulate as cells in culture or blooms age. This is the first report of the lethal effects of Scrippsiella trochoidea on shellfish larvae.     

<Emphasis Type="Italic">Cochlodinium polykrikoides</Emphasis> blooms and clonal isolates from the northwest Atlantic coast cause rapid mortality in larvae of multiple bivalve species

Globally, many commercial bivalve populations have declined in recent decades. In addition to overharvesting and habitat loss, the increasing frequency and intensity of harmful algal blooms (HABs) are likely to contribute to bivalve losses, particularly in cases where blooms negatively impact larval stages. This paper reports on the lethal effects of clonal cultures and blooms of Cochlodinium polykrikoides from the US Atlantic coast on the larvae of three species of commercially and ecologically valuable bivalves: the Eastern oyster (Crassostrea virginica), the bay scallop (Argopecten irradians), and the Northern quahog (hard clam; Mercenaria mercenaria). Both cultures and blooms of C. polykrikoides were highly toxic to all three species of bivalve larvae causing 80–100% mortality during 24- to 72-h exposures at concentrations of 1–2 × 10³ cells ml⁻¹. Toxicity was dependent on cell densities, growth stage of C. polykrikoides (i.e. cultures in exponential stage growth were more toxic than later stages), exposure time of larvae to cells (i.e. longer exposure caused higher mortality), the age of larvae (i.e. younger larvae were more sensitive), and the relative abundance of C. polykrikoides (i.e. the presence of other microalgae decreased toxicity). Free radical-scavenging enzymes (peroxidase and catalase) and the removal of C. polykrikoides cells (i.e. culture filtrate) significantly increased larval survival suggesting toxicity is maximized by contact with live cells and may involve labile toxins bound by these compounds including e.g. reactive oxygen species. The toxicity of C. polykrikoides to bivalve larvae was generally more severe than other HAB species (e.g. Karenia brevis, Karlodinium veneficum, Alexandrium tamarense, Prorocentrum minimum). Since the bivalves in this study spawn in the months when C. polykrikoides blooms on the east coast of North America, these results suggest that these blooms may have detrimental effects on efforts to restore these already diminished populations.     

RNA/DNA ratio and expression of 18S ribosomal RNA, actin and myosin heavy chain messenger RNAs in starved and fed larval Atlantic cod (Gadus morhua)

Levels of total RNA, total DNA, 18S ribosomal RNA (rRNA), poly(A) messenger RNA (mRNA), and two mRNAs coding for abundant myofibrillar proteins were estimated in laboratory-reared Atlantic cod larvae (Gadusmorhua Linnaeus) under conditions of feeding and starvation. DNA probes specific for cod 18S rRNA, β-actin mRNA and myosin heavy chain mRNA were developed. In two experiments on newly hatched larvae in fed and starved treatments, changes in 18S rRNA and mRNA were similar to changes in total RNA during the first weeks after hatching. RNA levels in fed and starved larvae in both experiments were stable, or increased, over the first 3 d after hatching, and then decreased to minima at 9 d. RNA levels increased after 9 d, with the degree and timing of the increase varying among the individual classes of RNA. Complete mortality of starved larvae in both experiments was observed shortly after 11 d, corresponding to exhaustion of endogenous yolk reserves. Total RNA content, RNA/DNA ratio, 18S rRNA levels, total mRNA pool, and actin and myosin heavy chain mRNA levels showed significant differences in fed and starved first-feeding larvae after yolk exhaustion. In another experiment with 3- to 4-week-old cod larvae, 18S rRNA levels were significantly lower in starved versus fed larvae after 3 d. Total RNA responded to feeding and starvation within a similar time as 18S rRNA and the mRNAs examined. Analysis of bulk nucleic acids using fluorometric dyes was simpler and faster than analysis of individual RNAs using hybridization probes, and provides valuable information on recent growth and condition of individual larvae. However, analysis of specific RNAs can provide information on expression of the corresponding genes and reveal the changes underlying trends seen in bulk RNA. Received: 9 February 1996 / Accepted: 7 June 1999     

Combined effects of temperature and salinity on fed and starved larvae of the mediterranean mussel Mytilus galloprovincialis and the Japanese oyster Crassostrea gigas

The combined effects of temperature, salinity and nutrition on survival and growth of larvae of the Mediterranean mussel Mytilus galloprovincialis and the Japanese oyster Crassostrea gigas were studied over a period of 7 d in the laboratory. Ripe adults, collected in spring and summer 1987 from natural populations in the Bay of Arcachon, France, were induced to spawn. Larvae of both species were cultured at four temperatures (15°, 20°, 25° and 30°C), four salinities (20, 25, 30 and 35S) per temperature, and two levels of nutrition (fed and unfed) per temperature/salinity combination. The fed larvae received a mixed algal diet of 50 cells each of Isochrysis galbana and Chaetoceros calcitrans forma pumilum per microlitre. In both bivalve species, larvae survived over a wide range of temperature and salinity, with the exception of mussel larvae, which died at 30°C. Statistical analysis indicated that nutrition had the greatest effect on larval development, explaining 64 to 75% of the variance in growth of M. galloprovincialis and 54 to 70% in growth of Crassostrea gigas. Unfed mussel larvae displayed little growth. Compared with temperature, the effect of salinity was very slight. M. galloprovincialis larvae exhibited best growth at 20°C and 35S and C. gigas at 30°C and 30S.     

Burrowing by the bivalve mollusc Lithophaga curta in the living reef coral Montipora berryi and a hypothesis of reciprocal larval recruitment

The burrowing bivalve Lithophaga curta is abundant (8 to 9 per 100 cm²) in the encrusting, hermatypic coral Montipora berryi at Enewetak; this is the first report of L. curta colonizing living coral. Conversely, larvae of M. berryi appear to settle in empty bivalve burrows, tentatively identified as those of L. curta, located in dead M. berryi. Several hypotheses are suggested on the adaptive significance of substrate selection by larvae of both species and an overall hypothesis of reciprocal recruitment, describing the dynamic aspects of this apparently co-evolved relationship, is proposed.     

Population genetic consequences of larval dispersal mode and hydrography: a case study with bryozoans

Genetic analysis of the marine bryozoans Celleporella hyalina and Electra pilosa using the RAPD technique revealed population structuring corresponding to the contrasting modes of larval dispersal. Samples of C. hyalina exhibited genetic differentiation over distances as small as 10 m, concordant with the limited dispersal predicted by a simulation model, based on the short pelagic phase of the lecithotrophic larvae and the local hydrography. In contrast, E. pilosa showed high levels of genetic heterogeneity only over much larger spatial scales, commensurate with its production of comparatively long-lived planktotrophic larvae. The population differentiation observed between samples of E. pilosa, collected from sites 70 km apart, is reconcilable with coastal water currents and frontal systems that restrict the exchange of water masses between the two sites. Hydrographic conditions and discontinuous distribution of suitable substrata therefore are seen to constrain gene flow, creating opportunities for local genetic differentiation despite the high dispersal potential of pelagic larvae. Received: 9 August 2000 / Accepted: 18 November 2000     

The culturable microbial community of the Great Barrier Reef sponge Rhopaloeides odorabile is dominated by an α-Proteobacterium

The microbial community cultured from the marine sponge Rhopaloeides odorabile Thompson et al. is dominated by a single bacterium, designated strain NW001. Sequence analysis of 1212 bp of the16S rRNA gene of strain NW001 indicates that it is a member of the α-subgroup of the class Proteobacteria. The association between this bacterium and its host sponge was observed in healthy R. odorabile collected from six different reefs in the Great Barrier Reef representing a geographic distance of 460 km, and in four collections in different seasons in 1997–1998 at Davies Reef (18°49.6′S; 147°34.49′E). The proportion of colonies of strain NW001 in samples from R. odorabile, expressed as a percentage of the total heterotrophic bacterial colony count, showed no significant spatial (range: 81–98%) or temporal differences (range: 81–99%), although colony counts of strain NW001 varied by up to two orders of magnitude between reef sites and sampling periods. The location of strain NW001 within the sponge mesohyl was visualized by in situ hybridization, using fluorescently labeled probes based on the 16S rRNA gene sequence of this strain. Cells of strain NW001 surround the choanocyte chambers, suggesting that these bacteria may play a role in nutrient uptake by the sponge. The absence of strain NW001 from corresponding seawater samples indicates that it has a specific, intimate relationship with R. odorabile and is not being utilized as a food source. A unique cyanobacterium related to the genera Leptolyngbya and Plectonema was also isolated from R. odorabile and characterized by 16S rRNA gene sequencing. Received: 19 May 2000 / Accepted: 18 November 2000