Specific gut bacterial responses to natural diets of tropical birds

The composition of gut bacterial communities is strongly influenced by the host diet in many animal taxa. For birds, the effect of diet on the microbiomes has been documented through diet manipulation studies. However, for wild birds, most studies have drawn on literature-based information to decipher the dietary effects, thereby, overlooking individual variation in dietary intake. Here we examine how naturally consumed diets influence the composition of the crop and cloacal microbiomes of twenty-one tropical bird species, using visual and metabarcoding-based identification of consumed diets and bacterial 16S rRNA microbiome sequencing. We show that diet intakes vary markedly between individuals of the same species and that literature-based dietary guilds grossly underestimate intraspecific diet variability. Furthermore, despite an effect of literature-based dietary guild assignment of host taxa, the composition of natural diets does not align with crop and cloacal microbiome similarity. However, host-taxon specific gut bacterial lineages are positively correlated with specific diet items, indicating that certain microbes associate with different diet components in specific avian hosts. Consequently, microbiome composition is not congruent with the overall consumed diet composition of species, but specific components of a consumed diet lead to host-specific effects on gut bacterial taxa.

Hoki (Macruronus novaezelandiae) Diet Variability and Associated Middle-Depth Demersal Fish Species Depth Distribution in the Ecosystem on the Chatham Rise, New Zealand.

<p>Fisheries management in New Zealand is mostly on a single species basis. Globally there is a shift towards multispecies or ecosystem based fisheries management. For this to happen an understanding of how the ecosystem is organised and functions is needed. Trophic food web and diet studies have been used effectively to begin to understand the functioning of marine ecosystems. Who eats whom, however, is not the full extent of ecosystem function. Understanding of species distribution patterns, of both predators and prey species are also needed to begin to understand the full function of the marine ecosystem. The first part of this study investigated the diet of hoki (Macruronus novaezelandiae) over the Chatham Rise, New Zealand, between 200-800m. It characterised the diet of hoki as well as investigated potential sources of diet variability. Hoki diet was found to consist largely of mesopelagic teleosts, mainly of the family Myctophidae, natant decapods and euphausids, suggesting a pelagic feeding strategy, as other studies have also found. Differences were found in diet composition between this study and other studies on hoki diet, potentially suggesting differences in prey distribution between study areas. Differences in diet were found between fish from different depths and different sized fish from the same depth. No consistent pattern of diet differences was found between the different areas studied, suggesting that the patterns found may be aliasing depth and size patterns as well as reflecting differences in hoki size class distribution. The distribution of hoki was not homogeneous over the study area, with small fish found mainly in the western part of the study area in shallower water, while large fish were predominately found at greater depths over the whole study area. The second part of this study looked at the overall species distribution of 30 demersal fish species over the Chatham Rise, specifically examining for evidence of the mid-domain effect. The study also investigated body-size depth trends between these species, and split by class Osteichthyes and Chondrichthyes. The mid-domain effect predicts species richness, and thus distribution, is due to geometric constraints with the greatest species richness to be found at the centre of a geographically constrained domain. The overall species distribution was found to be explained by the mid-domain effect. The distribution pattern of larger individuals being found in deeper water, with smaller individuals found in shallower water has often been seen in marine systems. We found no interspecific pattern for body-size depth distribution with the entire species assemblage, nor when the assemblage was split by class into Osteichthyes and Chondrichthyes, which supports our findings of the mid-domain effect. At a species level patterns of positive, negative and no trend were found with body-size depth relationships. At a community level species distribution over the studied depth range was largely explained by the geometric constraints of the mid-domain effect, while at a species level distribution over depth was often a reflection of body size. Some species had large individuals deep while other species had small. Overall this supports the hypothesis that competition or adaptation works more strongly at a population or species level, than on the overall community who's species distribution can more often be attributed to random chance. This study begins to explain predator species distribution over the Chatham Rise and looks at the diet of one dominant species in the Chatham Rise ecosystem. This provides some of the basic knowledge needed for fisheries management to move towards a more ecosystem based approach. Further research should include investigation into prey species distribution and abundance to clarify some of the questions raised in the diet part of this study about the cause of diet variability and whether it was related to either prey abundance or patchy prey distribution. Research into the diet of other fish would be useful to ascertain which species compete with hoki for food and would provide fisheries managers with a list of species that may be affected indirectly through changes in hoki quota of abundance.</p>

Hoki (Macruronus novaezelandiae) Diet Variability and Associated Middle-Depth Demersal Fish Species Depth Distribution in the Ecosystem on the Chatham Rise, New Zealand.

<p>Fisheries management in New Zealand is mostly on a single species basis. Globally there is a shift towards multispecies or ecosystem based fisheries management. For this to happen an understanding of how the ecosystem is organised and functions is needed. Trophic food web and diet studies have been used effectively to begin to understand the functioning of marine ecosystems. Who eats whom, however, is not the full extent of ecosystem function. Understanding of species distribution patterns, of both predators and prey species are also needed to begin to understand the full function of the marine ecosystem. The first part of this study investigated the diet of hoki (Macruronus novaezelandiae) over the Chatham Rise, New Zealand, between 200-800m. It characterised the diet of hoki as well as investigated potential sources of diet variability. Hoki diet was found to consist largely of mesopelagic teleosts, mainly of the family Myctophidae, natant decapods and euphausids, suggesting a pelagic feeding strategy, as other studies have also found. Differences were found in diet composition between this study and other studies on hoki diet, potentially suggesting differences in prey distribution between study areas. Differences in diet were found between fish from different depths and different sized fish from the same depth. No consistent pattern of diet differences was found between the different areas studied, suggesting that the patterns found may be aliasing depth and size patterns as well as reflecting differences in hoki size class distribution. The distribution of hoki was not homogeneous over the study area, with small fish found mainly in the western part of the study area in shallower water, while large fish were predominately found at greater depths over the whole study area. The second part of this study looked at the overall species distribution of 30 demersal fish species over the Chatham Rise, specifically examining for evidence of the mid-domain effect. The study also investigated body-size depth trends between these species, and split by class Osteichthyes and Chondrichthyes. The mid-domain effect predicts species richness, and thus distribution, is due to geometric constraints with the greatest species richness to be found at the centre of a geographically constrained domain. The overall species distribution was found to be explained by the mid-domain effect. The distribution pattern of larger individuals being found in deeper water, with smaller individuals found in shallower water has often been seen in marine systems. We found no interspecific pattern for body-size depth distribution with the entire species assemblage, nor when the assemblage was split by class into Osteichthyes and Chondrichthyes, which supports our findings of the mid-domain effect. At a species level patterns of positive, negative and no trend were found with body-size depth relationships. At a community level species distribution over the studied depth range was largely explained by the geometric constraints of the mid-domain effect, while at a species level distribution over depth was often a reflection of body size. Some species had large individuals deep while other species had small. Overall this supports the hypothesis that competition or adaptation works more strongly at a population or species level, than on the overall community who's species distribution can more often be attributed to random chance. This study begins to explain predator species distribution over the Chatham Rise and looks at the diet of one dominant species in the Chatham Rise ecosystem. This provides some of the basic knowledge needed for fisheries management to move towards a more ecosystem based approach. Further research should include investigation into prey species distribution and abundance to clarify some of the questions raised in the diet part of this study about the cause of diet variability and whether it was related to either prey abundance or patchy prey distribution. Research into the diet of other fish would be useful to ascertain which species compete with hoki for food and would provide fisheries managers with a list of species that may be affected indirectly through changes in hoki quota of abundance.</p>

Bioenergetic Model Sensitivity to Diet Diversity Across Space, Time and Ontogeny

Consumption is the primary trophic interaction in ecosystems and its accurate estimation is required for reliable ecosystem modeling. When estimating consumption, species’ diets are commonly assumed to be the average of those that occur among habitats, seasons, and life stages which introduces uncertainty and error into consumption rate estimates. We present a case study of a teleost (Yellowfin Bream Acanthopagrus australis) that quantifies the potential error in consumption (in mass) and growth rate estimates when using diet data from different regions and times and ignoring ontogenetic variability. Ontogenetic diet trends were examined through gut content analysis (n = 1,130 fish) and incorporated into a bioenergetic model (the “primary” model) that included diet variability (n = 144 prey sources) and ontogenetic changes in metabolism (1–7 year) to estimate lifetime consumption. We quantified error by building nine model scenarios that each incorporated different spatiotemporal diet data of four published studies. The model scenarios produced individual lifetime consumption estimates that were between 25% lower and 15% higher than the primary model (maximum difference was 53%, range 11.7–17.8 kg). When consumption (in mass) was held constant, differences in diet quality among models caused a several-fold range in growth rate (0.04–1.07 g day–1). Our findings showcase the large uncertainty in consumption rate estimates due to diet diversity, and illustrate that caution is required when considering bioenergetic results among locations, times, and ontogeny.