The influence of signal crayfish on fine sediment dynamics and macroinvertebrate communities in lowland rivers

The spread of non-native species is a global threat and the rate at which biological invasions occur is likely to increase in the future. This thesis examines the implications of the invasive signal crayfish, Pacifastacus leniusculus (Dana), for instream communities and abiotic processes within lowland rivers in England. The potential effects on lotic macroinvertebrate communities and fine sediment dynamics are investigated at a range of spatial and temporal scales, from the examination of national long-term datasets through to short-term detailed mesocosm experiments. Interrogation of macroinvertebrate community data from three English regions was undertaken to understand the temporal and spatial extent of signal crayfish effects. Invasive crayfish had significant long-term and persistent effects on resident macroinvertebrate communities regardless of the lithology or other environmental characteristics of the region. The resultant modifications to community composition had repercussions for several widely employed freshwater biomonitoring tools which employ faunal abundance in their derivation. A reach-scale field study was undertaken at two sites, one invaded by crayfish and one which did not support populations of crayfish (control), to assess the potential contribution of signal crayfish for fine sediment dynamics (ingress, fluxes and ultimately the overall implications for sediment budgets). Reach-scale field experiments examining the effect of crayfish invasion on resident macroinvertebrate communities over a 126-day period indicated that once crayfish populations are well-established their effects are persistent. However, separating the effects of crayfish from wider macroinvertebrate community dynamics and life-history characteristics of the invader and resident taxa means that attributing the effects is far from clear. The thesis presents the results of a series of novel mesocosm experiments which examined the dynamic and two-way interactions of predator-prey relationships and potential zoogeomorphological effects of signal crayfish and the freshwater shrimp, Gammarus pulex. Signal crayfish had a significant effect on the mass of fine sediment infiltrating into the gravel matrix associated with foraging and predatory activity; however this was strongly controlled by prey availability. Finally, through the development of conceptual models, the thesis illustrates the need for greater integration of ecological and geomorphological theories, at relevant environmental scales (temporal and spatial) to achieve truly interdisciplinary research

Fine sediment deposition and interstitial flow effects on macroinvertebrate community composition within riffle heads and tails

The distribution of macroinvertebrates in the heads and tails of riffles were examined in an in-situ field experiment under stable baseflow conditions. Paired colonisation cylinders were used to examine the influence of vertical hydraulic exchange (upwelling and downwelling) and horizontal interstitial flow on the patterns of sedimentation and invertebrate colonisation. Sedimentation rates were greatest in cylinders permitting vertical and horizontal flow (VHE cylinders) and were significantly lower (29%) in cylinders where only vertical flow and ingress of fine sediment were possible (VE cylinders). The results demonstrate that horizontal interstitial flows represent an important pathway for fine sediment transport. Differences in fine sediment accumulation were also observed between riffle heads and tails. Significantly higher sedimentation rates were recorded in riffle tails, with the macroinvertebrate communities characterised by larger proportions of fine sediment tolerant taxa. In contrast, riffle head communities were characterised by greater proportions of sediment sensitive taxa, and in the case of VHE cylinders, shredders and EPT taxa. The results demonstrate that spatial differences in fine sediment deposition are evident at the riffle scale as a function of vertical and horizontal subsurface flows and that these factors play a key role in the distribution of macroinvertebrate fauna

Investigating the role of a novel Type IV secretion system in Legionella pneumophila

A novel Type IV secretion system (T4SS) was identified in Legionella pneumophila isolates from the Edinburgh Legionnaires’ disease outbreak in 2012. A phylogenetic reconstruction of the isolates shows four distinct clades, two of which share a region thought to encode the novel T4SS. In a Galleria mellonella infection model, strains with this T4SS caused more rapid killing than those without it. Furthermore, patients infected with isolates containing the novel T4SS required more clinical care intervention. This project aims to dissect the role of the novel T4SS in intracellular survival. Bioinformatic analysis showed that the T4SS is closely related to the Legionella genomic island-associated T4SS (LGI-T4SS) of L. longbeachae. Other bioinformatic tools were used to identify neighbouring genes predicted to encode T4SS-secreted effector proteins. The expression of these genes was then detected during broth culture and intracellular growth using RT-PCR. A range of techniques were employed in order to compare the intracellular survival, replication and virulence of representative isolates from each of the four clades. Macrophage-like cells were infected in a gentamicin protection assay to compare intracellular replication. DNA extracted from the infected cells at four time points was quantified by qPCR to measure replication of the bacteria over time. In addition, the level of host cell death and autophagy was compared in macrophage-like cells infected with representative isolates from each clade. The results indicate that the region encoding the novel T4SS originated in L. longbeachae and encodes at least one putative T4SS effector protein. Although no difference was observed in host cell death and autophagy during infection with representative isolates, the presence of the novel region correlates with a reduced rate of intracellular replication

Temporal effects of enhanced fine sediment loading on macroinvertebrate community structure and functional traits

Deposition of fine sediment that fills interstitial spaces in streambed substrates is widely acknowledged to have significant negative effects on macroinvertebrate communities, but the temporal consistency of clogging effects is less well known. In this study the effects of experimentally enhanced fine sediment content on aquatic invertebrates were examined over 126 days in two lowland UK streams. Taxonomic approaches indicated significant differences in macroinvertebrate community structure associated with sediment treatment (clean or sedimented substrates), although the effects were variable on some occasions. The degree of separation between clean and sedimented communities was strong within 7 of the 9 sampling periods with significant differences in community composition being evident. EPT taxa and taxon characterised as sensitive to fine sediment demonstrated strong responses to enhanced fine sediment loading. In marked contrast, faunal traits did not facilitate the detection of enhanced fine sediment loading. More widely, the study highlights the temporal dynamics of sedimentation effects upon macroinvertebrate communities and the need to consider faunal life histories when examining the effects of fine sediment loading pressures on lotic ecosystems

Temporal variability in lotic macroinvertebrate communities associated with invasive signal crayfish (Pacifastacus leniusculus) activity levels and substrate character

Invasive signal crayfish (Pacifastacus leniusculus) are considered to be the most prevalent non-native crayfish species in Europe. Where large populations become established they have significant and long-term effects on benthic macroinvertebrate communities. However, much less is known about how community effects associated with crayfish invasion change in the short-term as a function of varying activity levels during the summer months. We examined the macroinvertebrate community composition of two lowland UK rivers, one which supported a well-established non-native crayfish population (invaded) and one in which crayfish had not been recorded (control). Colonisation cylinders were deployed which recorded community composition over a 126-day time period. Results indicate that once the activity period commences, invasive crayfish consistently altered macroinvertebrate community structure regardless of substrate character. Invaded communities displayed reduced beta-diversity compared to control sites. However, effects on the macroinvertebrate assemblage varied over the period when crayfish were active probably reflecting the behavioural activity of crayfish (which intensifies with increasing water temperature and during the spawning season) and life histories of other macroinvertebrates. The results indicate that crayfish invasions modify macroinvertebrate community composition, but over shorter timescales, the effects vary associated with their activity levels

Predator, prey and substrate interactions: the role of faunal activity and substrate characteristics

Many taxa possess a range of strategies to reduce the risk of predation, including actively seeking suitable refuge habitats; however, the global spread of invasive species may disrupt these behavioral responses. In lotic ecosystems, interstitial spaces in the substrate are important refugia for small organisms. Some predators are ecosystem engineers that exhibit zoogeomorphic agency—the ability to modify the geomorphology of their environment. It is therefore possible that direct ecological effects of predators on prey may be realized through modifications to the prey's habitat, including the availability of refugia, by predators that are zoogeomorphic agents or via external stressors such as fine sediment loading. This study examined three research questions in a mesocosm study across a gradient of sediment‐stress treatments: (1) What affects do predators (Pacifastacus leniusculus, invasive crayfish) and prey (Gammarus pulex, amphipods) have on the ingress of fine sediment into gravel substrates and therefore on available interstitial refugia? (2) Do prey taxa seek refuge from (invasive) predators in the form of vertical movement into subsurface sediments? and (3) How does fine sediment ingress influence predator–prey interactions and prey survival through predator avoidance behavior. Here, we provide direct evidence demonstrating that fine sediment ingress into gravel river beds can be facilitated by zoogeomorphic activity with P. leniusculus increasing the infiltration of fine sand particles (but not coarse sand) during foraging activities. Predator–prey interactions were found to be a primary factor mediating zoogeomorphic activity, with the isolation of crayfish from prey (G. pulex) leading to increased fine sand ingress. When present with signal crayfish, G. pulex displayed vertical avoidance behavior, entering subsurface substrates to evade predation by P. leniusculus. Coarse sand treatments resulted in higher predation rates of G. pulex, most likely due to clogging of interstitial pore spaces between gravels limiting the effectiveness of the prey's vertical avoidance behavior strategy. A new conceptual model that captures the interactions between predator, prey, zoogeomorphic processes and habitat availability is presented. This model highlights how predator–prey interactions can be strongly mediated by dynamic bi‐directional interactions between organisms and the physical environment they inhabit as ecological and geomorphological processes are intrinsically linked

Benthic and hyporheic macroinvertebrate distribution within the heads and tails of riffles during baseflow conditions

The distribution of lotic fauna is widely acknowledged to be patchy reflecting the interaction between biotic and abiotic factors. In an in-situ field study, the distribution of benthic and hyporheic invertebrates in the heads (downwelling) and tails (upwelling) of riffles were examined during stable baseflow conditions. Riffle heads were found to contain a greater proportion of interstitial fine sediment than riffle tails. Significant differences in the composition of benthic communities were associated with the amount of fine sediment. Riffle tail habitats supported a greater abundance and diversity of invertebrates sensitive to fine sediment such as EPT taxa. Shredder feeding taxa were more abundant in riffle heads suggesting greater availability of organic matter. In contrast, no significant differences in the hyporheic community were recorded between riffle heads and tails. We hypothesise that clogging of hyporheic interstices with fine sediments may have resulted in the homogenization of the invertebrate community by limiting faunal movement into the hyporheic zone at both the riffle head and tail. The results suggest that vertical hydrological exchange significantly influences the distribution of fine sediment and macroinvertebrate communities at the riffle scale

Discharge and suspended sediment time series as controls on fine sediment ingress into gravel river beds

Fine sediment availability and channel hydraulics are two of the primary controls on the ingress of fine sediment into gravel river beds. A novel dataset consisting of fine sediment ingress measurements coupled with high-resolution turbidity and discharge time series, was analysed to investigate relations between ingress, discharge and turbidity. Discharge and turbidity demonstrated a weak association with each other, and their relations with fine sediment ingress were relatively weak. An alternative, but widely applied ‘redundancy’ approach was investigated that focused on key metrics, or facets, of the discharge and turbidity time series and their association with fine sediment ingress. Principal component analysis was used to distil the most important facets driving variation in the discharge and turbidity datasets and these were then used as independent variables in regression models with sediment ingress as the dependent variable. These models accounted for a larger amount of the statistical variation in sediment ingress over time than discharge and turbidity time series. Facets of the turbidity time series were found to be the most effective explanatory variables. The results suggest that this approach could be valuable and justify its application and testing across a range of river types in different hydrological and sedimentary settings. Application of this method could improve our generic understanding of what controls ingress at larger spatial and temporal scales and therefore complements process-based approaches, which is vital for the development of fine sediment management strategies

The importance of biotic entrainment for base flow fluvial sediment transport

Sediment transport is regarded as an abiotic process driven by geophysical energy, but zoogeomorphological activity indicates that biological energy can also fuel sediment movements. It is therefore prudent to measure the contribution that biota make to sediment transport, but comparisons of abiotic and biotic sediment flux are rare. For a stream in the UK, the contribution of crayfish bioturbation to suspended sediment flux was compared with the amount of sediment moved by hydraulic forcing. During baseflow periods, biotic fluxes can be isolated because nocturnal crayfish activity drives diel turbidity cycles, such that night-time increases above day-time lows are attributable to sediment suspension by crayfish. On average, crayfish bioturbation contributed at least 36% (430 kg) to monthly baseflow suspended sediment loads; this biotic surcharge added between 4.7 and 13.54 t (0.19 to 0.55 t km-2 yr-1) to the annual sediment yield. As anticipated, most sediment was moved by hydraulic forcing during floods and the biotic contribution from baseflow periods represented between 0.43 and 1.24% of the annual load. Crayfish activity is nonetheless an important impact during baseflow periods and the measured annual contribution may be a conservative estimate because of unusually prolonged flooding during the measurement period. In addition to direct sediment entrainment by bioturbation, crayfish burrowing supplies sediment to the channel for mobilization during floods so that the total biotic effect of crayfish is potentially greater than documented in this study. These results suggest that in rivers, during baseflow periods, bioturbation can entrain significant quantities of fine sediment into suspension with implications for the aquatic ecosystem and baseflow sediment fluxes. Energy from life rather than from elevation can make significant contributions to sediment fluxes