The biodiversity of two distinct marine environments was observed to describe the biogeocomplexity of these extreme ecological systems. A shallow-water hydrothermal vent in Papua New Guinea served as a study of a thermophilic ecosystem influenced by arsenic rich vent fluids while a 60 m deep offshore primarily anoxic karst sink served as a study of an anaerobic sulfur-influenced habitat. Both environments support unique biological communities that are influenced by the physical and chemical pressures imposed on them by the harsh conditions of these systems. In Tutum Bay, Ambitle Isle, Papua New Guinea, a transect was created from a shallow hydrothermal vent that extended 120 m away from the vent. Previous studies have shown that the geochemistry of the system is heavily influenced by arsenic which is toxic to most organisms. In this study, macro- and meiofauna were collected and scored and combined with bacterial sequence data collected along the length of the transect. It was found that near vent sites harbored biological communities more similar than sites further from the vent. Many species were found only at sites near the hydrothermal vent. Near-vent communities were less diverse than those away from the vent, and biodiversity generally increased as distance from the vent increased. Distinct correlations between thermophilic organisms and temperature were observed. The metabolic repertoire of the microbial communities suggests that many strategies are used to obtain energy and carbon. The relative abundance of bacteria containing genes to reduce arsenic was comparable to those able to reduce sulfur compounds. Primary production appeared to be a mix of chemo- and phototrophy. Food webs and association analysis suggest a complex interplay between macrofaunal, meiofaunal and bacterial communities. While the system is heavily influenced by arsenic, no specific correlation between the relative abundance of arsenic metabolizing organisms and the amount of arsenic in the system could be drawn. This is likely due to the fact that most of the arsenic produced by the system is readily adsorbed onto iron oxyhydroxides, reducing the arsenic's bioavailability. The anoxic conditions at Jewfish sink provide a different hurdle than the hot arsenic conditions found in Papua New Guinea. The anoxic conditions are shared by other pit features found in karst geography, but the metabolic processes between Jewfish sink and these other karst habitats are different. The blue holes and black holes of the Bahamas are some of the most well-studied of these karstic pits. In these features, which are large circular pits with diameters of over 300 m, light and sulfur are used as a means of energy acquisition. Jewfish sink, having an opening only 6 m in diameter, is light restricted compared to these systems. As a result, the strategy of organisms dwelling in the anoxic conditions of the sink is different than those found at the well-studied holes in the Bahamas. Geochemical measurements were recorded over two time periods spanning a combined total of 6 years. The anoxic bottom waters of Jewfish sink remain stable and contained high levels of sulfide throughout most of the seasons studies. Sequence analysis of prokaryotes within the sink showed that sulfur reducers had the highest relative abundance compared to other functional guilds. To monitor the changes of the microbial communities within the sink, bacterial communities were examined at 4 depths within the sink at 9 different intervals over a period of 685 days. Denaturing Gradient Gel Electrophoresis (DGGE) was used to fingerprint 16s rRNA bacterial communities and dissimilatory sulfite reducing communities by targeting the 16s rRNA bacterial gene and the dsr gene associated with dissimilatory sulfite reducing bacteria and archaea. The lowest depth studied within the sink (40 m) remained stable chemically and biologically until a turnover event occurred within the second winter of the study. This turnover event disrupted the biological communities at 40 m and led to a reestablished community comprised of different species that those found prior to the event. Upper waters within the sink show that clines establish themselves seasonally and partition zones that confine bacterial communities that are more similar to each other within these zones while excluding bacterial communities that are outside of these zones. Oxygenated water was shown to not contain prokaryotes containing the dsr gene. As the oxycline changed seasonally, dissimilatory sulfite reducing prokaryotes containing the dsr gene remained in the anoxic zone and required time to reestablish themselves whenever oxygenated water displaced them.

Shallow-water hydrothermal vents occur world-wide in regions of volcanic activity. The vents located at Tutum Bay, Ambitle Island, Papua New Guinea are unique in that the vent fluids and surrounding sediments contain some of the highest concentrations of arsenic in a natural system. This study addresses the effects of the vent system on the benthic communities, focusing on the eukaryotes, macrofauna, meiofauna and bacteria. Samples were collected in November 2003 and May/June 2005. Analysis of the 2003 macrofaunal samples indicated that pH, rather than arsenic was influencing the benthic community, and that the hydrothermal influence occurred at a greater distance than expected. Results of more intensive sampling carried out in 2005 are the primary focus of this dissertation. The pore water and sediment characteristics revealed distinct physical habitats corresponding with distance from the vent. There was a trend of decreasing temperature and arsenic concentration and increasing salinity and pH with distance from the vent. The vent sediment was poorly sorted volcanic gravel, while sediments along the transect showed a gradient from fine, well sorted volcanic sands to coarser carbonate sands farther away. The macrofauna showed a trend of increasing diversity with distance from the vent and similar taxa were present in both the 2003 and 2005 samples. The vent community was dominated by the polychaete Capitella cf. capitata. The inner transect from 30 m to 140 m had low diversity. Dominant taxa included thalassinid shrimp and the amphipod Platyischnopus sp.A. The 180 m to 300 m sites had significantly higher diversity. The Danlum Bay reference site had relatively higher diversity than the nearshore transect sites and was dominated by deposit feeding polychaetes. Macrofaunal community structure was influenced by the sediment characteristics, notably by CaCO3 content, sorting and median grain size. The meiofaunal community also showed changes with distance from the vent. Chromadorid nematodes were dominant at the vent site and were a major component of the meiofauna at most sites, along with copepods. The meiofaunal community at the reference site showed greater similarity to the vent community and both sites had low abundances. Nematodes were more abundant than copepods near the vent, but copepods were more abundant farther offshore and at the reference site. Meiofaunal community structure was influenced primarily by the pore water temperature and salinity. Biological interactions with the macrofaunal community through physical disturbance and predation may also influence the meiofaunal community.  The molecular analysis of eukaryotic and bacterial diversity also revealed changes with distance from the vent. The 0 m and reference sites grouped together due to the presence of fungal sequences and the 140 m and 300 m sites grouped together due to a common molluscan sequence. Metazoans and fungi dominated the eukaryote sequences. The most abundant eukaryotic OTUs included fungi matching Paecilomyces sp. and Cladosporium cladosporioides and metazoans matching Viscosia viscosa (Nematoda) and Astarte castanea represented by 24 phyla and was dominated by Actinobacteria and γ-Proteobacteria. More bacterial phyla were present near the vent, while more overall OTUs were found at the intermediate sites along the transect. The most distant site had much lower diversity dominated by Firmicutes. The macrofaunal community had the strongest correlation with environmental variables. Comparison between the meiofauna and the metazoan sequences showed the proportion of nematodes found in both datasets were comparable, but the meiofauna analysis found a higher proportion of arthropods, while the molecular results were disproportionally high for platyhelminthes. Overall, the vents increased the complexity of the system by creating unique habitats. The extreme environment created by the hydrothermal activity maintained the surrounding habitat at an early successional stage colonized by a few opportunistic species. There was a gradation in the benthic communities away from the vent towards a more carbonate based climax community. The low pH environment had an effect on the sediment composition, which in turn influenced the benthic community. These findings can serve as a model for studying the potential effects of ocean acidification and climate change on benthic communities and marine biocomplexity.