A decade of change in the Skidaway River estuary I. Hydrography and nutrients

Estuarine microbial networks and relationships vary between environmentally distinct communities

Microbial interactions have profound impacts on biodiversity, biogeochemistry, and ecosystem functioning, and yet, they remain poorly understood in the ocean and with respect to changing environmental conditions. We applied hierarchical clustering of an annual 16S and 18S amplicon dataset in the Skidaway River Estuary, which revealed two similar clusters for prokaryotes (Bacteria and Archaea) and protists: Cluster 1 (March-May and November-February) and Cluster 2 (June-October). We constructed co-occurrence networks from each cluster to explore how microbial networks and relationships vary between environmentally distinct periods in the estuary. Cluster 1 communities were exposed to significantly lower temperature, sunlight, NO₃, and SiO₄; only NH₄ was higher at this time. Several network properties (e.g., edge number, degree, and centrality) were elevated for networks constructed with Cluster 1 vs. 2 samples. There was also evidence that microbial nodes in Cluster 1 were more connected (e.g., higher edge density and lower path length) compared to Cluster 2, though opposite trends were observed when networks considered Prokaryote-Protist edges only. The number of Prokaryote-Prokaryote and Prokaryote-Protist edges increased by >100% in the Cluster 1 network, mainly involving Flavobacteriales, Rhodobacterales, Peridiniales, and Cryptomonadales associated with each other and other microbial groups (e.g., SAR11, Bacillariophyta, and Strombidiida). Several Protist-Protist associations, including Bacillariophyta correlated with Syndiniales (Dino-Groups I and II) and an Unassigned Dinophyceae group, were more prevalent in Cluster 2. Based on the type and sign of associations that increased in Cluster 1, our findings indicate that mutualistic, competitive, or predatory relationships may have been more representative among microbes when conditions were less favorable in the estuary; however, such relationships require further exploration and validation in the field and lab. Coastal networks may also be driven by shifts in the abundance of certain taxonomic or functional groups. Sustained monitoring of microbial communities over environmental gradients, both spatial and temporal, is critical to predict microbial dynamics and biogeochemistry in future marine ecosystems.

Temporal Variability and Ecological Interactions of Parasitic Marine Syndiniales in Coastal Protist Communities

Syndiniales are a ubiquitous group of protist parasites that infect and kill a wide range of hosts, including harmful bloom-forming dinoflagellates. Despite the importance of parasitism as an agent of plankton mortality, parasite-host dynamics remain poorly understood, especially over time, hindering the inclusion of parasitism in food web and ecosystem models. For a full year in the Skidaway River Estuary (Georgia), we employed weekly 18S rRNA sampling and co-occurrence network analysis to characterize temporal parasite-host infection dynamics of Syndiniales. Over the year, Syndiniales exhibited strong temporal variability, with higher relative abundance from June to October (7 to 28%) than other months in the year (0.01% to 6%). Nonmetric dimensional scaling of Syndiniales composition revealed tight clustering in June to October that coincided with elevated temperatures (23 to 31°C), though in general, abiotic factors poorly explained composition (canonical correspondence analysis [CCA] and partial least-squares [PLS]) and were less important in the network than biotic relationships. Syndiniales amplicon sequence variants (ASVs) were well represented in the co-occurrence network (20% of edges) and had significant positive associations (Spearman r > 0.7), inferred to be putative parasite-host relationships, with known dinoflagellate hosts (e.g., Akashiwo and Gymnodinium) and other protist groups (e.g., ciliates, radiolarians, and diatoms). Positive associations rarely involved a single Syndiniales and dinoflagellate species, implying flexible parasite-host infection dynamics. These findings provide insight into the temporal dynamics of Syndiniales over a full year and reinforce the importance of single-celled parasites in driving plankton population dynamics. Further empirical work is needed to confirm network interactions and to incorporate parasitism within the context of ecosystem models.IMPORTANCE Protist parasites in the marine alveolate group, Syndiniales, have been observed within infected plankton host cells for decades, and recently, global-scale efforts (Tara Ocean exploration) have confirmed their importance within microbial communities. Yet, protist parasites remain enigmatic, particularly with respect to their temporal dynamics and parasite-host interactions. We employed weekly 18S amplicon surveys over a full year in a coastal estuary, revealing strong temporal shifts in Syndiniales parasites, with highest relative abundance during warmer summer to fall months. Though influenced by temperature, Syndiniales population dynamics were also driven by a high frequency of biological interactions with other protist groups, as determined through co-occurrence network analysis. Parasitic interactions implied by the network highlighted a range of confirmed (dinoflagellates) and putative (diatoms) interactions and suggests parasites may be less selective in their preferred hosts. Understanding parasite-host dynamics over space and time will improve our ability to include parasitism as a loss term in microbial food web models.

Hyalophysa lynni n. sp. (Ciliophora, Apostomatida), a new pathogenic ciliate and causative agent of shrimp black gill in penaeid shrimp

The parasitic ciliate causing shrimp black gill (sBG) infections in penaeid shrimp has been identified. The sBG ciliate has a unique life cycle that includes an encysted divisional stage on the host's gills. The ciliature of the encysted trophont stage has been determined and is quite similar to that of the closely related apostomes Hyalophysa bradburyae and H. chattoni. Hyalophysa bradburyae is a commensal ciliate associated with freshwater caridean shrimp and crayfish, while H. chattoni is a common commensal found on North American marine decapods. Based on 18S rRNA gene sequence comparisons, the sBG ciliate is more closely related to the marine species H. chattoni than to the freshwater species H. bradburyae. The unique life cycle, morphology, 18S rRNA gene sequence, hosts, location, and pathology of the sBG ciliate distinguish this organism as a new species, Hyalophysa lynni n. sp.

Evaluation of long-term trends in hydrographic and nutrient parameters in a southeast US coastal river

The Nassau River estuary is located in northeast Florida adjacent to the eutrophic St. Johns River. Historically, development has been sparse in the Nassau River's catchment; thus, the system may provide a relatively undisturbed aquatic environment. To monitor the condition of the Nassau River estuary and to discern spatial and temporal trends in water quality, nutrients and hydrographic variables were assessed throughout the estuary from 1997 to 2011. Hydrographic (temperature, salinity, total suspended solids, and turbidity) and nutrient parameters (total phosphorus, ortho-PO₄(3-), total nitrogen, NH₄(+), total Kjeldahl nitrogen, and NO₃(-)) were monitored bimonthly at 12 sites in the mesohaline and polyhaline zones of the river. Nonparametric Kendall's Tau was implemented to analyze long-term water quality patterns. Salinity was found to increase with time, particularly in the mesohaline sampling sites. Dissolved oxygen decreased over time in the estuary and hypoxic conditions became increasingly frequent in the final years of the study. Nutrients increased in the estuary, ranging from 149 to 401%. Rainfall data collected in adjacent conservation areas did not correlate well with nutrients as compared with stream discharge data collected in the basin headwaters, outside of the conservation lands, attributed here to expanding urbanization. During the study period, the Nassau basin underwent rapid human population growth and land development resulting in commensurate impacts to water quality. Nutrient and physical data collected during this study indicate that the Nassau River estuary is becoming more eutrophic with time.

The occurrence, spatial and temporal distribution, and environmental routes of tetracycline resistance and integrase genes in Crassostrea virginica beds

Rapid spread of antibiotic resistance genes has placed them under consideration as emerging environmental contaminants. The occurrence and distribution of tetracycline resistance genes (TRG) and integrons (INT) have been monitored for 2 years in seven oyster beds located in the Altamaha River (Georgia, USA) estuary. TRG/INT profiles varied both temporally (p<0.025) and spatially between oysters and their environment (p<0.005) suggesting shifts in sources of contamination and selection of TRG/INT carriers by oysters. The latter was confirmed via analysis of tet(D) and tet(G) distribution between oysters and their environment. Uncommon class 3 integrons dominated the integrons' profile in oysters. The frequency of TRG/INT incidents correlated (R(2) ≥ 0.9) to (i) dissolved solids, (ii) potential water density, and (iii) turbidity but not to the amount of local precipitation suggesting the watershed as the dominant source of TRG/INT contamination and other than directly rainfall-caused run-offs as its environmental route.

Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage

Quantitative PCR (qPCR) analysis revealed elevated relative abundance (1.8% of prokaryotes) of marine group 1 Crenarchaeota (MG1C) in two samples of southeastern US coastal bacterioplankton, collected in August 2008, compared with samples collected from the same site at different times (mean 0.026%). We analyzed the MG1C sequences in metatranscriptomes from these samples to gain an insight into the metabolism of MG1C population growing in the environment, and for comparison with ammonia-oxidizing bacteria (AOB) in the same samples. Assemblies revealed low diversity within sequences assigned to most individual MG1C open reading frames (ORFs) and high homology with 'Candidatus Nitrosopumilus maritimus' strain SCM1 genome sequences. Reads assigned to ORFs for ammonia uptake and oxidation accounted for 37% of all MG1C transcripts. We did not recover any reads for Nmar_1354-Nmar_1357, proposed to encode components of an alternative, nitroxyl-based ammonia oxidation pathway; however, reads from Nmar_1259 and Nmar_1667, annotated as encoding a multicopper oxidase with homology to nirK, were abundant. Reads assigned to two homologous ORFs (Nmar_1201 and Nmar_1547), annotated as hypothetical proteins were also abundant, suggesting that their unknown function is important to MG1C. Superoxide dismutase and peroxiredoxin-like transcripts were more abundant in the MG1C transcript pool than in the complete metatranscriptome, suggesting an enhanced response to oxidative stress by the MG1C population. qPCR indicated low AOB abundance (0.0010% of prokaryotes), and we found no transcripts related to ammonia oxidation and only one RuBisCO transcript among the transcripts assigned to AOB, suggesting they were not responding to the same environmental cues as the MG1C population.

Population growth away from the coastal zone: thirty years of land use change and nutrient export in the Altamaha River, GA

We used more than thirty years of water quality monitoring data collected by the United States Geological Survey at several stations in the Altamaha River and its tributaries to examine the relationship between population density, agricultural land use, and nutrient export from the watershed. Population densities in the Altamaha River watershed increased during the study period, most notably in the upper watershed near metropolitan Atlanta, while agricultural land use declined throughout the watershed. NO(x), TN and P in rivers were related to human population densities, while OC and NH(4)(+) concentrations in rivers were apparently related to agricultural land use. A general pattern of increasing NO(x) and TN and decreasing NH(4)(+), P and OC over time throughout the watershed reflected changing population and land use. The overall average load from the Altamaha River to the coastal zone during the study period was 1.1, 5.6, 16.9, 0.9 and 262 kmol km(-2) yr(-1), delivering 40, 197, 596, 30, and 9213.10(6) mol yr(-1) of NH(4)(+), NO(x), TN, P and OC, respectively, to the coastal zone. The nutrient export patterns suggest that N and P loading to rivers in the Altamaha River watershed was greatest in the upper watershed where high population densities were found, and in-stream processing, dilution, and only moderate inputs during transit through the lower watershed resulted in relatively low export from the watershed to coastal waters.

Bioluminescent bacteria as indicators of chemical contamination of coastal waters

The ratio of bioluminescent to total bacteria (bioluminescent ratio, BLR) as an indicator of a variety of types of anthropogenic contamination of estuarine ecosystems was evaluated through a series of laboratory and field studies. Laboratory studies indicated that the BLR of natural bacterioplankton communities was proportionally reduced in the presence of a number of contaminants including diesel fuel and saltmarsh sediments co-contaminated with mercury and polychlorinated biphenyls (PCBs). Bioluminescent ratio inhibition was observed after short-term exposure to a contaminant suggesting a physiological rather than a population response of native microbial communities. Simulated eutrophication did not suppress the BLR. Field observations of the BLR were conducted weekly for a 2-yr period in the Skidaway River estuary, Georgia, USA. These observations revealed considerable seasonal variability associated with the BLR. Bioluminescent ratios were highest during the summer (25 +/- 15%), lower in the fall (6 +/- 5%) and spring (3 +/- 2%), and near zero during the winter. Although the BLR was not significantly correlated to salinity at a single site (Skidaway River estuary), the BLR was significantly correlated with salinity when sites within the same estuary system were compared (r2 = 0.93). Variation in BLR was not correlated to standard bacteriological indicators of water quality including total and fecal coliform bacteria. Comparison of the BLR from impacted and pristine estuarine sites during the fall suggested that anthropogenically impacted sites exhibited lower BLR than predicted from salinity versus BLR relationships developed in pristine systems. These observations suggest that the BLR could be used as a simple and reliable initial indicator of chemical contamination of estuarine systems resulting from human activity.