The structure and composition of microbial communities inhabiting the soft coral Alcyonium antarcticum were investigated across 3 differentially contaminated sites within McMurdo Sound, Antarctica - McMurdo Station (MM), Scott Base (SB) and Cape Armitage (CA).Samples from all sites were subjected to culture-based analysis, denaturing gradient gel electrophoresis (DGGE), 16S rRNA gene clone-library analysis, and (FISH).Phylogenetic groups included Gamma-, Alpha- and Beta- proteobacteria; Bacteroidetes; Firmicutes; Actinomycetales; Planctomycetes; and Chlorobi and bacteria from the functional group of sulfate-reducing bacteria. To investigate the structure and composition of microbial communities inhabiting the soft coral Alcyonium antarcticum.To examine any variation within and between Alcyonium antarcticum bacterial communities from 3 differentially contaminated sites within McMurdo Sound, Antarctica . This was the first investigation of microbial communities associated with Antarctic soft corals.Accession numbers assigned to sequencing products: Culture1-Culture10 (DG312224, DG312225, DG312226, DG312227, DG312228, DG312229, DG312230, DG312231, DG312232, DG312233); OTU1-OTU15 (DG312234, DG312235, DG312236, DG312237, DG312238, DG312239, DG312240, DG312241, DG312242, DG312243, DG312244, DG312245, DG312246, DG312247, DG312248); DGGE Band1-Band11, (DG312249, DG312250, DG312251, DG312252, DG312253, DG312254, DG312255, DG312256, DG312257, DG312258) and Band14-Band16 (DG312259, DG312260, DG312261).

Specimens of the marine sponge Rhopaloeides odorabile (class Demospongiae; order Dictyoceratida; family Spongiidae) were collected from Davies Reef and Lizard Island on the Great Barrier Reef (3 from each location).Molecular techniques were employed to document the microbial diversity associated with the marine sponge Rhopaloeides odorabile.The phylogenetic affiliation of sponge-associated bacteria was assessed by 16S rRNA sequencing of cloned DNA fragments. Fluorescence in situ hybridization (FISH) was used to confirm the presence of the predominant groups indicated by 16S rDNA analysis. Novel media incorporating sponge extracts were used to isolate bacteria not previously recovered from this sponge.A radial cladogram was constructed showing the diversity of bacterial clone sequences from R. odorabile. Neighbor-joining phylogenetic trees were constructed from analyses of: 823 bp of 16S rRNA gene sequence included 34 clones for which unique sequence was obtained;709 bp of 16S rRNA gene sequence from clones clustering with the Actinobacteria;804 bp of 16S rRNA gene sequence from clones clustering within the predominantly g-Proteobacteria;811 bp of 16S rRNA gene sequence from clones clustering with green nonsulfur bacteria and d-Proteobacteria;305 bp of 16S rDNA sequence obtained from organisms cultured using sponge extract media.Branches were also found using the Fitch-Margoliash and maximum parsimony methods. The effects of using actinomycete-selective media supplemented with sponge extract on total number and the number of novel bacterial morphotypes isolated from R. odorabile were measured. Medium preparations were: marine agar 2216; starch-casein agar; Emerson agar; raffinose-histidine agar; M31 Casamino Acids agar; actinomycete isolation agar; yeast-malt extract agar; and glycerol-asparagine agar. The effects of stress, including copper exposure and elevated sea temperatures on the sponge microbial community were assessed. These impacts cause a distinct shift in the microbial community including a move away from symbiosis towards disease-causing microbes.Community structure included representatives of the Actinobacteria, low-GC Gram-positive bacteria, the b- and g-subdivisions of the Proteobacteria, Cytophaga/Flavobacterium, green sulfur bacteria, green nonsulfur bacteria, planctomycetes, and other sequence types with no known close relatives. The study aimed to investigate the diversity of the total bacterial community within the sponge R. odorabile.

The Australian Collection of Antarctic Microorganisms (ACAM) was established in 1986 at the University of Tasmania as a collection for microorganisms from the Antarctic continent as well as from subantarctic islands and the Southern Ocean. ACAM is one of the few collections in the world dedicated to the collection of Antarctic bacteria and since its inception has grown to nearly 400 strains. Many of these strains have been isolated from lakes and marine waters in the Vestfold Hills region of Antarctica near Davis Station. Salinity, redox potential, light and temperature all vary dramatically between these water bodies and, on many occasions, have been shown to vary with water depth within them. Microorganisms living in these ecosystems cope with a variety of physical extremes which characterise the Antarctic environment. The potential for biotechnological use of Antarctic microorganisms has become more evident from basic studies on the taxonomy and molecular biology of antarctic microbes. Recently, bacteria have been isolated that (i) contain polyunsaturated w-3 fatty acids, (ii) degrade hydrocarbons (including polycyclic aromatics) and (iii) produce bioactive natural products. ACAM is a continually expanding collection. The search for Antarctic microorganisms that may be commercially exploited has only just begun. Future research should identify novel strains that offer further potential for biotechnology and, at the same time, provide a better understanding of the Antarctic ecosystem. ACAM is now available through the Australian Antarctic Data Centre's Biodiversity database, or via the ACAM website. This work was completed as part of ASAC project 65 (ASAC_65).

During the central and eastern Torres Strait survey in November 2006, tissue samples of 10 individuals of the sponge Coscinoderma matthewsi were collected from 5 island groups: Ugar (Stephen Island) and Erub (Darnley Island) in eastern Torres Strait; and the Masig group (Kodall Island and Keats Island), Poruma (Coconut Island) and Warraber (Sue Island) in central Torres Strait. These island groups are on average, 66 km apart. All sponge samples were placed in separate cryo-tubes and preserved in liquid nitrogen until they could be stored at -80°C. Approximately 2 g of tissue from each sample was homogenised in liquid nitrogen and 750 µl of lysis buffer [100 mM Tris pH 9, 100 mM EDTA, 1% SDS, 100 mM NaCl, 0.5 mg/ml Proteinase K], and subsequently incubated at 65°C for 1 hour with gentle agitation. KoAc was added to a final concentration of 1 M, followed by incubation on ice for 30 minutes. The samples were centrifuged at 8000 rpm for 15 minutes, and the supernatant was reserved for DNA precipitation with isopropanol using the standard protocol.A fragment of nuclear DNA containing part of the 28S rRNA gene was amplified for all individuals using RD3A (5'-GACCCGTCTTGAAACACGA) and RD5B2 (5'- ACACACTCCTTAGCGGA) primers. Recombinant Pfu Polymerase (Fermentas) was used for the PCR. A total of 50 µl of reaction mixture was prepared for each sample according to the protocol. PCR was performed under the following conditions: initial denaturation at 95°C for 3 minutes; 35 cycles of 95°C for 30 seconds, 50°C for 20 seconds, 72°C for 1 minute; a final extension step of 72°C for 10 minutes. Products were purified with QIAquick (Qiagen) columns according to protocol. Sequencing was performed at Macrogen Inc. with a 3730xl DNA analyser using both forward and reverse primers.For microbial analysis, a DNA fingerprinting technique (denaturing gradient gel electropohoresis - DGGE) was used to determine the stability of bacterial associations within Coscinoderma matthewsi across wide spatial scales.Four replicate sponges were analysed from Keats Island and Kodall Island and three replicate sponges were analysed from Erub, Ugar, Poruma and Warraber. DNA was extracted from individual sponges by homogenising approx 1g of tissue from each individual in 0.5 ml of grinding buffer (2 ml 1 M Tris, 4 ml 0.5M EDTA, 2 ml 10% SDS, 400 µl 5 M NaCl and 11.6 ml distilled water). Tubes were immersed in liquid nitrogen and ground with plastic pestles. Samples were incubated at 65ºC for 60 min prior to addition of 187 µl 5 M potassium acetate. Samples were incubated on ice for 30 min and centrifuged at 8000 x g for 15 min. The supernatants were transferred to fresh tubes and DNA was precipitated with 0.8 vol of isopropanol.The 16S rDNA from each sample was amplified by PCR with universal bacterial primers 1055f: 5'-ATG GCT GTC GTC AGC T-3' and 1406r: 5'-ACG GGC GGT GTG TAC-3'. The reverse primer was modified to incorporate a 40 bp GC clamp. Primers 1055f and 1406r match over 56,000 and 62,800 sequences respectively in the Ribosomal Database Project. Products from triplicate PCR reactions were combined and 15 µl applied to duplicate 40% wt/vol polacrylamide (37:5:1) gels containing a 50-70% denaturing gradient of formamide and urea. Gels were electrophoresed at 60ºC for 17 h in 1 x TAE buffer at 50V using the Ingeny D-Code system. Gels were stained with 1 x Sybr Gold for 30 min, visualised under UV illumination and photographed. This project was undertaken to determine connections between sponge populations in central and eastern Torres Strait and to assess whether there would be any risks associated with translocation of sponges across large areas. Risks investigated were the possibility of transfers between genetically distinct populations, which would result in a decrease in the genetic diversity of wild populations or the potential to introduce new sponge-associated microbe types into a region.

This study presents compelling evidence for a diverse and abundant seabed community which has developed over the course of the Holocene beneath the Amery Ice Shelf in East Antarctica. Fossil analysis of a 47 cm long sediment core reveals a rich modern fauna, dominated by filter feeders (sponges and bryozoans), with an abundant infauna predominantly of polychaetes. The down-core assemblage reveals a succession in the colonisation of this site. The lower portion of the core (prior to ~9600 yr BP) is completely devoid of preserved fauna. The first colonisers of the site after this time were the mobile benthic organisms. Their occurrence in the core is matched by the first appearance of planktonic taxa, indicating a retreat of the ice shelf following the last glaciation to within sufficient distance to advect planktonic particles via bottom currents. The benthic infauna and filter feeders emerged during the peak abundance of the planktonic organisms, indicating their dependence on this advected food supply which is brought via bottom currents flowing from the open shelf waters of Prydz Bay. Understanding patterns of species succession in this environment has important implications for determining the potential significance of future global change. The collapse of Antarctic ice shelves, as has happened in recent times, would significantly change the organic supply regime, and therefore the nature of these sub-ice shelf benthic communities.

This study presents compelling evidence for a diverse and abundant seabed community which has developed over the course of the Holocene beneath the Amery Ice Shelf in East Antarctica. Fossil analysis of a 47 cm long sediment core reveals a rich modern fauna, dominated by filter feeders (sponges and bryozoans), with an abundant infauna predominantly of polychaetes. The down-core assemblage reveals a succession in the colonisation of this site. The lower portion of the core (prior to ~9600 yr BP) is completely devoid of preserved fauna. The first colonisers of the site after this time were the mobile benthic organisms. Their occurrence in the core is matched by the first appearance of planktonic taxa, indicating a retreat of the ice shelf following the last glaciation to within sufficient distance to advect planktonic particles via bottom currents. The benthic infauna and filter feeders emerged during the peak abundance of the planktonic organisms, indicating their dependence on this advected food supply which is brought via bottom currents flowing from the open shelf waters of Prydz Bay. Understanding patterns of species succession in this environment has important implications for determining the potential significance of future global change. The collapse of Antarctic ice shelves, as has happened in recent times, would significantly change the organic supply regime, and therefore the nature of these sub-ice shelf benthic communities.