Stopover habitat selection drives variation in the gut microbiome composition and pathogen acquisition by migrating shorebirds

Long-distance host movements play a major regulatory role in shaping microbial communities of their digestive tract. Here, we studied gut microbiota composition during seasonal migration in five shorebird species (Charadrii) that use different migratory (stopover) habitats. Our analyses revealed significant interspecific variation in both composition and diversity of gut microbiome, but the effect of host identity was weak. A strong variation in gut microbiota was observed between coastal and inland (dam reservoir and river valley) stopover habitats within species. Comparisons between host age classes provided support for an increasing alpha diversity of gut microbiota during ontogeny and an age-related remodeling of microbiome composition. There was, however, no correlation between microbiome and diet composition across study species. Finally, we detected high prevalence of avian pathogens, which may cause zoonotic diseases in humans (e.g. Vibrio cholerae) and we identified stopover habitat as one of the major axes of variation in the bacterial pathogen exposure risk in shorebirds. Our study not only sheds new light on ecological processes that shape avian gut microbiota, but also has implications for our better understanding of host-pathogen interface and the role of birds in long-distance transmission of pathogens.

Variation in resource use between adult and juvenile Semipalmated Sandpipers (Calidris pusilla) and use of physiological indicators for movement decisions highlights the importance of small staging sites during southbound migration in Atlantic Canada

Semipalmated Sandpipers (Calidris pusilla) are Arctic-breeding shorebirds that use staging sites in Atlantic Canada during their annual migration to South America. The Bay of Fundy has long been recognized as a critical staging site for migrating Semipalmated Sandpipers and supports a large prey base. The diet of adult sandpipers in the Bay is flexible but the diet of juveniles, which arrive later, is not well documented. Comparatively little is known about the prey base and how it is utilized by sandpipers at sites in Atlantic Canada outside the Bay. Plasma metabolite measures can provide useful insight to assess habitat quality for sandpipers and have not yet been measured in Semipalmated Sandpipers in Atlantic Canada. To address these knowledge gaps we sampled shorebird habitat to estimate invertebrate availability in the Bay of Fundy and the Northumberland Strait. Concurrently, we collected blood samples from adult and juvenile sandpipers for analysis of plasma metabolite levels and isotopic estimates of dietary niche in both regions. We found that sites on the Northumberland Strait hosted a more diverse and variable prey base than sites within the Bay of Fundy, and that sandpipers were selective when foraging there, appearing to prefer bivalves. Juveniles may occupy a broader dietary niche than adults along the Northumberland Strait, though appear to gain weight as efficiently. Sandpipers sampled along the Northumberland Strait had higher plasma triglyceride concentrations than those within the Bay of Fundy, which may suggest differences in fattening rate or dietary fat intake. Sandpipers that had lower triglyceride concentrations on the Northumberland Strait were more likely to move into the Bay of Fundy, while sandpipers with high triglyceride values tended to remain on the Strait. These data suggest that sandpipers made movement decisions within the region depending on their physiological state. Our results suggest adult and juvenile Semipalmated Sandpipers successfully use a variety of staging habitats in Atlantic Canada. This is an encouraging finding for sandpiper conservation in the region, but also indicates that maintaining access to a broad variety of staging habitats is critical, supporting calls for stronger conservation measures throughout the region.

Length of stay and departure strategies of Semipalmated Sandpipers (Calidris pusilla) during post-breeding migration in the upper Bay of Fundy, Canada

The Bay of Fundy, Canada is a critical staging area for Semipalmated Sandpipers (Calidris pusilla) during post-breeding migration. Recent range-wide population declines and changes in diet and migratory timing in the Bay of Fundy prompted a re-examination of staging ecology, including length of stay (last estimated in 1981), which is used in calculating migratory population estimates. We used radio-telemetry and the Motus Wildlife Tracking System to estimate individual length of stay and departure conditions for 159 Semipalmated Sandpipers in 2013 and 2014. Using tracking data we compared two estimation methods, minimum length of stay and mark-recapture modelling. Using minimum length of stay, the mean length of stay was approximately 21 days, an increase from the previous estimate of 15 days. Mark-recapture models suggested a much longer staging period that is inconsistent with other data. Sandpipers captured early in the staging period stayed longer on average than those captured later. Departures from the staging area were correlated with north-westerly winds, moderate to high wind speeds and low but rising atmospheric pressures. We suggest that Semipalmated Sandpipers in the Bay of Fundy are not operating on a time-selected migration schedule and instead wait for favourable weather conditions to depart, which occur more often later in the migratory period. Population trends in the Bay of Fundy should be re-evaluated in light of the increased length of stay.

Influences of submerged plant collapse on diet composition, breadth, and overlap among four crane species at Poyang Lake, China

Background

Interannual variation in resource abundance has become more unpredictable, and food shortages have increasingly occurred in the recent decades. However, compared to seasonal fluctuations in resource abundance, the influences of interannual variation in resource abundance on the dietary niches of consumers remain poorly understood. Poyang Lake, China, is a very important wintering ground for the globally endangered Siberian Crane (Leucogeranus leucogeranus), White-naped Crane (Grus vipio), and Hooded Crane (G. monacha), as well as the non-endangered Eurasian Crane (G. grus). Tubers of Vallisneria spp., the dominant submerged macrophytes at Poyang Lake, is an important food for cranes. Nevertheless, submerged macrophytes have experienced serious degradation recently. In this study, we used metabarcoding technology to explore the consequences of Vallisneria tuber collapse on the diet compositions, breadths, and overlaps of the four crane species based on fecal samples collected in winter 2017 (a year with tuber collapse) and winter 2018 (a year with high tuber abundance).

Results

Compared to previous studies, our study elucidates crane diets in an unprecedented level of detail. Vallisneria tubers was confirmed as an important food source of cranes. Surprisingly, the grassland plant Polygonum criopolitanum was also found to be an important food source in the feces of cranes. Agricultural fields were important foraging sites for Siberian Cranes, White-naped Cranes, and Hooded Cranes, providing foods that allowed them to survive in winters with natural food shortages. However, the three crane species preferred natural wetlands to agricultural fields when the abundance of natural foods was high. The abundance of Vallisneria tubers, and probably P. criopolitanum, greatly influenced the dietary compositions, breadths and overlap of cranes. During periods of preferred resource shortage, White-naped Cranes and Hooded Cranes widened their dietary niches, while Siberian Cranes maintained a stable niche width. The dietary niche overlap among crane species increased substantially under conditions of plentiful preferred food resources.

Conclusions

Our study emphasizes the superior quality of natural wetlands compared to agricultural fields as foraging habitats for cranes. To provide safer and better foraging areas for cranes, it is urgent to restore the submerged plants at Poyang Lake. While high dietary niche overlap is often interpreted as intense interspecific competition, our study highlights the importance of taking food abundance into account.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12983-021-00411-2.

The influence of migration patterns on exposure to contaminants in Nearctic shorebirds: a historical study

Since the 1970s, many populations of shorebirds, including those breeding in the Arctic region, have been declining. One factor that may contribute to some of these declines is exposure to contaminants throughout the annual cycle. Here, we compared contaminant exposure (organochlorines, toxic trace elements) of four Arctic-breeding shorebirds (semipalmated plover Charadrius semipalmatus, semipalmated sandpiper Calidris pusilla, lesser yellowlegs Tringa flavipes, and short-billed dowitcher Limnodromus griseus), collected during breeding, migration, and wintering to examine how and when contaminants might pose a threat to these species. In general, plovers and dowitchers had higher levels of most organochlorine pesticides, and renal cadmium (Cd) and selenium (Se) than the other species. Although we found seasonal differences, no clear patterns in contaminant concentrations among sampling locations were detected but the concentrations found at the breeding grounds were always the highest for chlorinated pesticides and mercury (Hg). Our results suggest that birds migrating south are slowly depurating contaminant burdens, and that spring-migrating birds were exposed to primarily North American rather than Latin American contaminant sources at the time of sampling. We present these data collected in the 1990s to better interpret current-day trends, and potential contaminant exposure impacts on shorebird populations.

Composition and Drivers of Gut Microbial Communities in Arctic-Breeding Shorebirds

Gut microbiota can have important effects on host health, but explanatory factors and pathways that determine gut microbial composition can differ among host lineages. In mammals, host phylogeny is one of the main drivers of gut microbiota, a result of vertical transfer of microbiota during birth. In birds, it is less clear what the drivers might be, but both phylogeny and environmental factors may play a role. We investigated host and environmental factors that underlie variation in gut microbiota composition in eight species of migratory shorebirds. We characterized bacterial communities from 375 fecal samples collected from adults of eight shorebird species captured at a network of nine breeding sites in the Arctic and sub-Arctic ecoregions of North America, by sequencing the V4 region of the bacterial 16S ribosomal RNA gene. Firmicutes (55.4%), Proteobacteria (13.8%), Fusobacteria (10.2%), and Bacteroidetes (8.1%) dominated the gut microbiota of adult shorebirds. Breeding location was the main driver of variation in gut microbiota of breeding shorebirds (R² = 11.6%), followed by shorebird host species (R² = 1.8%), and sampling year (R² = 0.9%), but most variation remained unexplained. Site variation resulted from differences in the core bacterial taxa, whereas rare, low-abundance bacteria drove host species variation. Our study is the first to highlight a greater importance of local environment than phylogeny as a driver of gut microbiota composition in wild, migratory birds under natural conditions.

Fatty acid composition and concentration of alternative food of Semipalmated Sandpipers (Calidris pusilla) in the upper Bay of Fundy, Canada

Semipalmated Sandpipers (Calidris pusilla (L., 1766)) that migrate through the upper Bay of Fundy, Canada, depend on a rich food supply to fuel their continued migration. Although past studies have reported a diet dominated by the amphipod Corophium volutator (Pallas, 1766), an animal rich in n–3 polyunsaturated fatty acids (PUFAs), recent evidence suggests that sandpiper diets are broad. This is beneficial in that it allows Semipalmated Sandpipers to respond to a changing food base, but quality of food is also important. PUFAs are important in providing the energy required by migrating birds and may play a role in migratory preparation. We assessed fatty acid (FA) concentrations and proportions in three common food items. We found that polychaetes should adequately meet the needs of migrating sandpipers in terms of FA composition. Concentrations of FAs in biofilm were low, but proportionally, n–3 PUFAs were well represented, particularly in biofilm collected in Shepody Bay, where it forms a substantial part of the sandpiper diet. Therefore, provided that birds can consume a sufficient volume of biofilm, it is also probably a suitable source of essential FAs. Our results suggest that Semipalmated Sandpipers in the Bay of Fundy can meet their FA needs with a variety of dietary options.

Biofilm consumption and variable diet composition of western sandpipers (Calidris mauri) during migratory stopover

Many shorebird species undertake long-distance migrations punctuated by brief stays at food-rich, estuarine stopover locations. Understanding use of these food resources helps guide conservation and responsible development decisions. We determined the extent and degree to which Western Sandpiper (Calidris mauri) utilized biofilm as a food resource across a large and variable stopover location during northward (spring) migration. We investigated the spatial heterogeneity in diet composition, to determine whether shorebirds were consistently feeding on biofilm or whether diet varied between naturally and anthropogenically delineated sites. We used stable isotope analysis to estimate that biofilm conservatively comprised 22% to 53% of Western Sandpiper droppings across all sampling sites and that prey composition differed significantly between areas within the stopover location. Widespread biofilm consumption demonstrates the importance of biofilm as a dietary component. Variable diet composition suggests that habitat heterogeneity may be an important component of high quality stopover locations in the context of “state-dependant trade-offs” of Western Sandpiper population sub-groups. Future management decisions must consider and address potential impacts on the biofilm community throughout a stopover location, as single site studies of diet composition may not be adequate to develop effective management strategies for entire stopover sites.

Behavioral response of Corophium volutator to shorebird predation in the upper Bay of Fundy, Canada

Predator avoidance is an important component of predator-prey relationships and can affect prey availability for foraging animals. Each summer, the burrow-dwelling amphipod Corophium volutator is heavily preyed upon by Semipalmated Sandpipers (Calidris pusilla) on mudflats in the upper Bay of Fundy, Canada. We conducted three complementary studies to determine if adult C. volutator exhibit predator avoidance behavior in the presence of sandpipers. In a field experiment, we monitored vertical distribution of C. volutator adults in bird exclosures and adjacent control plots before sandpipers arrived and during their stopover. We also made polymer resin casts of C. volutator burrows in the field throughout the summer. Finally, we simulated shorebird pecking in a lab experiment and observed C. volutator behavior in their burrows. C. volutator adults were generally distributed deeper in the sediment later in the summer (after sandpipers arrived). In August, this response was detectably stronger in areas exposed to bird predation than in bird exclosures. During peak predator abundance, many C. volutator adults were beyond the reach of feeding sandpipers (>1.5 cm deep). However, burrow depth did not change significantly throughout the summer. Detailed behavioral observations indicated that C. volutator spent more time at the bottom of their burrow when exposed to a simulated predator compared to controls. This observed redistribution suggests that C. volutator adults move deeper into their burrows as an anti-predator response to the presence of sandpipers. This work has implications for predators that feed on burrow-dwelling invertebrates in soft-sediment ecosystems, as density may not accurately estimate prey availability.

Antipredator vigilance decreases with food density in staging flocks of Semipalmated Sandpipers (Calidris pusilla)

When animals face time constraints, antipredator vigilance is expected to decrease in patches with higher food density. Indeed, sacrifices in safety are worthwhile in rich food patches that allow substantial foraging gains in response to a decrease in vigilance. This prediction has received little empirical attention. I tested this prediction in fall-staging Semipalmated Sandpipers (Calidris pusilla (L., 1766)) using the frequency of looks while foraging as a proxy for vigilance. Fall-staging sandpipers face time constraints, as individuals must accumulate fat rapidly before undertaking their long migration south. Controlling for known correlates of vigilance, such as distance to obstructive cover, bird density, and position in the flock, the frequency of looks decreased as predicted when the density of food in a patch was higher. That vigilance can vary with food density is relevant for observational studies of vigilance. When food density is positively correlated with group size, food density can become a confounding factor in the well-known negative relationship between vigilance and group size.

Staging ecology of Semipalmated Plover (Charadrius semipalmatus) and Semipalmated Sandpiper (Calidris pusilla) juveniles in the St. Lawrence River Estuary during fall migration

The acquisition of body reserves by migrating shorebirds at specific staging sites is critical for reaching their breeding or wintering grounds. As many North American shorebird populations are declining, major staging sites need to be identified for effective conservation plans. Changes in body mass of Semipalmated Plover (Charadrius semipalmatus Bonaparte, 1825) and Semipalmated Sandpiper (Calidris pusilla (L., 1766)) juveniles, as well as length of stay and daily movements by Semipalmated Plover juveniles during fall migration, were studied in the St. Lawrence River Estuary in southern Quebec, Canada. Most juveniles of both species captured early in the migration period weighed less than the estimated mean fat-free mass. Body mass increased steadily in juveniles of both species during staging. Mean body masses of birds captured in our study area were similar to or higher than those of juveniles of both species captured along the North Atlantic coast. Length of stay of radio-tracked Semipalmated Plover juveniles ranged from 2 to 28 days. Body mass at capture and length of stay were negatively associated, suggesting that individuals refuelled before resuming their migration. Overall, these results provide evidence that the St. Lawrence River Estuary is an important staging site for Semipalmated Plover and Semipalmated Sandpiper juveniles.

Mercury and methylmercury bioaccumulation by polychaete worms is governed by both feeding ecology and mercury bioavailability in coastal mudflats

Polychaete worms are abundant in many mudflats but their importance to coastal food web Hg biomagnification is not known. We sampled sediments and polychaete worms from mudflats in the Bay of Fundy to investigate the bioaccumulation of mercury (Hg) and methylmercury (MeHg) in the coastal invertebrate food web. Hg concentrations in the sediments were low (<20 μg kg(-1)). Labile Hg (methanol/KOH sediment extraction) in surface sediments (0-1 cm) was positively correlated with Hg bioaccumulation by surface sediment-ingesting polychaetes but, surprisingly, there was a negative correlation between δ(15)N (i.e. trophic level) and THg bioaccumulation factors in polychaete worms. Worms feeding on deeper sediments contained the greatest MeHg concentrations (69.6 μg kg(-1)). Polychaetes are an important vector for Hg biomagnification to the coastal avian food web. This research demonstrates that feeding depth and method of feeding are more important than trophic position or sediment Hg concentrations for predicting Hg bioaccumulation.