The primary focus of this thesis is to identify the changes in meiofauna community structure in response to the estuarine salinity gradient. This was achieved through morphological identification of the nematode phylum to species level in parallel with DNA barcoding of the whole meiofauna community and associated microscopic benthic fauna and flora. This is the first study to simultaneously identify environmental samples of nematode species and meiofauna taxa diversity using morphology-based and DNA barcoding methods, and reports an accurate correspondence between the two techniques.
Benthic diversity along the salinity gradient is predicted by Remane (1934) to show a decline in species richness from both freshwater and marine salinities to a species minimum at the mid estuary, between 3 and 8 psu. This model also predicts that changes in community composition occur along the salinity gradient and divided the community by salinity tolerance into freshwater, brackish (from 3 to 18 psu) and marine species. Morphology-based nematode species richness and DNA barcoding-derived nematode diversity and whole community 18S OTU (3% cut-off) diversity all supported the Remane (1934) pattern of diversity along the salinity gradient, exhibiting a cubic functional form. Meiofauna diversity decreased with distance from both freshwater and marine salinities and reached a diversity minimum between 6 to 11 psu.
Nematode community composition, based on both morphological and genetic analyses, whole meiofauna community (genetic analyses only) and community maturity along the estuary were influenced by salinity, to the exclusion of all other variables. Although community composition and dominance were shown to shift along the salinity gradient, no specific brackish water community sensu Remane (1934) was distinguished. The nematode communities of low (< 5 psu), mid (5 to 18 psu) and high (> 18 psu) salinity zones were however distinguishable in terms of composition, using both morphology-based species and OTU (3%) community composition. Differences in community structure among salinity zones were greater than those among estuaries. The community within each salinity zone was analysed independently to better identify the influence of other environmental variables and distinguish these from the effects of salinity. The influence of salinity was palpable even after disassembly into the low, mid and high salinity zones, as the proportion of distance to the estuary mouth (overall highly correlated with salinity) still explained most variation in the mid and high zone communities, in addition to organic carbon and copper content in the mid zone and lead content in the high salinity zone. The influence of mean particle size was found to be strongest in the low salinity zone.
Community diversity along the salinity gradient reflected variation in salinity, pollution load and the number of metal thresholds (Effects Range-Low, ERL) exceeded. Low salinity zone diversity variation was correlated with variation in mean particle size and measures of station trophic quality, whereas high salinity zone diversity was related to salinity, the relative distance
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to the estuary mouth and measures of trophic quality. Mid salinity zone diversity was not explained by any combination of environmental variables, however, diversity of a mid salinity station sampled over two years was structured by water content, sediment temperature, organic carbon content, total nitrogen content, normalised zinc concentrations and the pollution load index (PLI).
Indicator species were identified, including the first record of Koerneria pararmata in the UK and Ireland. This indicator species occurred in stations under elevated nutrient and organic enrichment pressure between the salinity range of 0.2 to 10.0 psu, which extended to 16 psu during the temporal study. Axonolaimus spinosus and Dorylaimus stagnalis were indicator species of lower trophic quality in low salinity zone stations, Sabatieria pulchra and Terschellingia communis in the mid zone and T.communis, T.longicaudata and Metachromadora vivipara were indicators of reduced trophic quality in the high salinity zone.
Temporal variation in this community among seasons and its reactions to changing salinity over time were assessed through the bimonthly study of one mid-estuary station for a period of two years. Temporal trends in diversity with changing salinity tended to complement the pattern observed spatially, but with reduced diversity at those summer time points at which water content and organic content were reduced. Although the temporal study did not cover a period necessary to establish seasonal patterns conclusively (3 - 5 years; Coull 1999), seasonal changes within the community were observed. Species richness and average taxonomic distinctness were substantially lower at peak summer time-points and assemblages at these summer time-points differed from those in winter and autumn. Despite such variability, temporal changes in community similarity were less pronounced than spatial changes among stations.
In summary, these investigations lay the foundations for long-term ecological monitoring of transitional water systems. Although future studies may be based on either morphological or genetic analyses, this thesis concludes that a combination of the two methods will provide higher quality and more robust data than either alone to accelerate our understanding of these complex benthic ecosystems.

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SAFER-Data Display URL	https://eparesearch.epa.ie/safer/iso19115/display?isoID=3001
Resource Keywords	meiofauna, estuaries, biodiversity, bar-coding, WFD
EPA/ERTDI/STRIVE Project Code	2007-PhD-B-4
EPA/ERTDI/STRIVE Project Theme	Biodiversity
Resource Availability:	Semi-Private
Limitations on the use of this Resource	Acknowledgement required if used. Please consult data holder if primary data required.
Number of Attached Files (Publicly and Openly Available for Download):	0
Project Start Date	Wednesday 28th November 2007 (28-11-2007)
Earliest Recorded Date within any attached datasets or digital objects	Sunday 29th June 2008 (29-06-2008)
Most Recent Recorded Date within any attached datasets or digital objects	Monday 28th June 2010 (28-06-2010)
Published on SAFER	Wednesday 30th January 2013 (30-01-2013)
Date of Last Edit	Wednesday 30th January 2013 at 09:55:17 (30-01-2013)
Datasets or Files Updated On	Wednesday 30th January 2013 at 09:55:17 (30-01-2013)

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Description of Geographical Characteristics of This Project or Dataset
Transitional waters east coast of Ireland from oligohaline to polyhaline zones. Estuaries sampled were Castletown, Boyne, Rogerstown, Broadmeadow, Bull Island and Wexford.

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