scholarly journals A novel bioaugmentation technique effectively increases the skin-associated microbial diversity of captive eastern hellbenders

2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Erin K Kenison ◽  
Obed Hernández-Gómez ◽  
Rod N Williams
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
River Water ◽  
Community Composition ◽  
Alpha Diversity ◽  
Natural Environments ◽  
Population Declines ◽  
In Captivity ◽  
In The Wild ◽  
Future Work

Abstract Captive environments are maintained in hygienic ways that lack free-flowing microbes found in animals’ natural environments. As a result, captive animals often have depauperate host-associated microbial communities compared to conspecifics in the wild and may have increased disease susceptibility and reduced immune function. Eastern hellbenders (Cryptobranchus alleganiensis alleganiensis) have suffered precipitous population declines over the past few decades. To bolster populations, eastern hellbenders are reared in captivity before being translocated to the wild. However, the absence of natural microbial reservoirs within the captive environment diminishes the diversity of skin-associated bacteria on hellbender skin and may negatively influence their ability to defend against pathogenic species once they are released into the wild. To prepare hellbenders for natural bacteria found in riverine environments, we devised a novel bioaugmentation method to increase the diversity of skin microbial communities within a captive setting. We exposed juvenile hellbenders to increasing amounts of river water over 5 weeks before translocating them to the river. We genetically identified and phylogenetically compared bacteria collected from skin swabs and river water for alpha (community richness) and beta (community composition) diversity estimates. We found that hellbenders exposed to undiluted river water in captivity had higher alpha diversity and distinct differentiation in the community composition on their skin, compared to hellbenders only exposed to well water. We also found strong evidence that hellbender skin microbiota is host-specific rather than environmentally driven and is colonized by rare environmental operational taxonomic units in river water. This technique may increase hellbender translocation success as increasing microbial diversity is often correlated with elevated disease resistance. Future work is necessary to refine our methods, investigate the relationship between microbial diversity and hellbender health and understand how this bioaugmentation technique influences hellbenders’ survival following translocation from captivity into the wild.

scholarly journals Influence of Seaweed Supplements on the Intestinal Bacteria in the Rabbitfish Siganus Fuscescens: Evidence for a Core Microbiome

2020 ◽  
Author(s):  
Valentin Thepot ◽  
Joel Slinger ◽  
Michael A Rimmer ◽  
Nicholas A Paul ◽  
Alexandra H Campbell
Keyword(s):  
Alpha Diversity ◽  
Intestinal Bacteria ◽  
Taxonomic Resolution ◽  
Control Fish ◽  
Human Pathogens ◽  
Farmed Fish ◽  
Core Microbiome ◽  
In Captivity ◽  
In The Wild ◽  
Future Work

Abstract BackgroundWe know very little about natural variation in microbiomes of marine herbivorous fish in the wild or in captivity (aquaculture). Understanding how the consumption of seaweed influences intestinal microbial communities will shed light on how such phytobiotics could enhance the health and productivity of farmed fish. Here we screened the effects of supplementing the diets of mottled rabbitfish (Siganus fuscescens), a candidate species for international aquaculture development, with 15 different species of seaweeds and functional supplements currently used in aquaculture, on the bacterial communities that colonised their hindguts. ResultsRemarkably, the second most abundant phylum and the majority (53%) of the bacterial genera were not assigned, highlighting a significant knowledge gap for the field of animal microbiomes. Dietary supplementation increased alpha diversity by up to 23% relative to the control fish. Furthermore, most supplements significantly increased the relative abundance of Firmicutes, with similar trends for Proteobacteria and consistent decreases in Bacteroides. Seaweed supplementation also had important effects at the genus level, including significant increases in Fusobacterium sp. in fish fed seaweed - especially the green Caulerpa taxifolia – and overall trends for reduced levels of Arcobacter sp., a genus that includes fish and human pathogens. When we compared microbiomes in our fish to those from two recently published studies of conspecific populations sampled many thousands of kilometres away, the populations were clearly distinct, however there were 55 ASVs that were shared across the three fish populations, of which 35 were present in 50% of all fish sampled.ConclusionThe identification of a core microbiome suggests that a host organism relies on certain microbes for key functions and our findings suggest that this candidate aquaculture species has a core microbiome in its hindgut which is robust to dietary manipulations and broad geographical and temporal variation. This insight will help guide future work investigating the functional and mechanistic bases of these relationships, as will improvements in microbial taxonomic resolution. Supplementation with seaweeds did have subtle influences on bacteria in the hindgut of Siganus fuscescens which could have important impacts on fish health and should be considered as aquaculture systems are developed for this species.

scholarly journals Impacts of Shade Trees on the Adjacent Cacao Rhizosphere in a Young Diversified Agroforestry System

Agronomy ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 195
Author(s):  
Jennifer E. Schmidt ◽  
Alana Firl ◽  
Hamran Hamran ◽  
Nur Insana Imaniar ◽  
Taylor M. Crow ◽  
...  
Keyword(s):  
Soil Fertility ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Community Composition ◽  
Early Stage ◽  
Agroforestry System ◽  
Agroforestry Systems ◽  
Shade Trees ◽  
Nitrogen And Phosphorus ◽  
Shade Tree

Cacao agroforestry systems offer the potential to diversify farmer income sources, enhance biodiversity, sequester carbon, and deliver other important ecosystem services. To date, however, studies have emphasized field- and system-scale outcomes of shade tree integration, and potential impacts on the rhizosphere of adjacent cacao trees have not been fully characterized. Interactions at the root–soil interface are closely linked to plant health and productivity, making it important to understand how diverse shade tree species may affect soil fertility and microbial communities in the cacao rhizosphere. We assessed the impacts of neighboring shade tree presence and identity on cacao yields and physical, chemical, and biological components of the cacao rhizosphere in a recently established diversified agroforestry system in South Sulawesi, Indonesia. Stepwise regression revealed surprising and strong impacts of microbial diversity and community composition on cacao yields and pod infection rates. The presence of neighboring shade trees increased nitrogen, phosphorus, and pH in the rhizosphere of nearby cacao trees without yield losses. Over a longer time horizon, these increases in rhizosphere soil fertility will likely increase cacao productivity and shape microbial communities, as regression models showed nitrogen and phosphorus in particular to be important predictors of cacao yields and microbiome diversity and composition. However, neither presence nor identity of shade trees directly affected microbial diversity, community composition, or field-scale distance-decay relationships at this early stage of establishment. These results highlight locally specific benefits of shade trees in this agroecological context and emphasize the rhizosphere as a key link in indirect impacts of shade trees on cacao health and productivity in diversified systems.

scholarly journals Captivity systematically alters the composition yet not the diversity of vertebrate gut microbiomes

2021 ◽  
Author(s):  
Antton Alberdi ◽  
Garazi Martin ◽  
Ostaizka Aizpurua
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
New Taxa ◽  
Meta Analysis ◽  
Similar Amount ◽  
Vertebrate Species ◽  
In Captivity ◽  
Open Debate ◽  
In The Wild ◽  
Compositional Changes

Abstract There is an open debate on whether and how captivity alters the gut microbiota of vertebrates, due to the contrasting results reported in different taxa and the absence of systematic multi-species analyses. We performed a meta-analysis of gut microbiota profiles of 322 captive and 322 wild specimens from 24 vertebrate species, including fish, reptiles, amphibians and mammals. We found no evidence that captivity either systematically depletes or increases their gut microbiota. In 88% of the species analysed, although captivity entailed a loss of a fraction of the diversity found in the wild, this was compensated through recruitment of a proportionally similar amount of new taxa only found in captivity. We show such compositional changes can impact evolutionary and ecological inferences that rely on hierarchical clustering-based comparative analyses of gut microbial communities across species.

scholarly journals Captivity causes taxonomic and functional convergence of gut microbial communities in bats

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6844 ◽  
Author(s):  
Yanhong Xiao ◽  
Guohong Xiao ◽  
Heng Liu ◽  
Xin Zhao ◽  
Congnan Sun ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Animal Species ◽  
Rhinolophus Ferrumequinum ◽  
Kegg Pathways ◽  
Functional Convergence ◽  
Rdna Sequencing ◽  
In Captivity ◽  
In The Wild ◽  
The Impact ◽  
Rule Out

Background Diet plays a crucial role in sculpting microbial communities. Similar diets appear to drive convergence of gut microbial communities between host species. Captivity usually provides an identical diet and environment to different animal species that normally have similar diets. Whether different species’ microbial gut communities can be homogenized by a uniform diet in captivity remains unclear. Methods In this study, we compared gut microbial communities of three insectivorous bat species (Rhinolophus ferrumequinum, Vespertilio sinensis, and Hipposideros armiger) in captivity and in the wild using 16S rDNA sequencing. In captivity, R. ferrumequinum and V. sinensis were fed yellow mealworms, while H. armiger was fed giant mealworms to rule out the impact of an identical environment on the species’ gut microbial communities. Results We found that the microbial communities of the bat species we studied clustered by species in the wild, while the microbial communities of R. ferrumequinum and V. sinensis in captivity clustered together. All microbial functions found in captive V. sinensis were shared by R. ferrumequinum. Moreover, the relative abundances of all metabolism related KEGG pathways did not significantly differ between captive R. ferrumequinum and V. sinensis; however, the relative abundance of “Glycan Biosynthesis and Metabolism” differed significantly between wild R. ferrumequinum and V. sinensis. Conclusion Our results suggest that consuming identical diets while in captivity tends to homogenize the gut microbial communities among bat species. This study further highlights the importance of diet in shaping animal gut microbiotas.

scholarly journals A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease

2021 ◽  
Vol 11 ◽  
Author(s):  
Lydia Luise Bach ◽  
Asha Ram ◽  
Umer Z. Ijaz ◽  
Thomas J. Evans ◽  
Jan Lindström
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Common Core ◽  
Temporal Stability ◽  
Alpha Diversity ◽  
Molecular Techniques ◽  
Human Pathogens ◽  
Healthy Human ◽  
Culture Independent ◽  
Over Time

Our understanding of human microbial communities, in particular in regard to diseases is advancing, yet the basic understanding of the microbiome in healthy subjects over time remains limited. The oropharynx is a key target for colonization by several important human pathogens. To understand how the oropharyngeal microbiome might limit infections, and how intercurrent infections might be associated with its composition, we characterized the oropharyngeal microbiome of 18 healthy adults, sampled weekly over a 40-weeks using culture-independent molecular techniques. We detected nine phyla, 202 genera and 1438 assignments on OTU level, dominated by Firmicutes, Bacteroidetes, and Proteobacteria on phylum level. Individual microbiomes of participants were characterized by levels of high alpha diversity (mean = 204.55 OTUs, sd = 35.64), evenness (19.83, sd = 9.74) and high temporal stability (mean Pearson’s correlation between samples of 0.52, sd = 0.060), with greater differences in microbiome community composition between than within individuals. Significant changes in community composition were associated with disease states, suggesting that it is possible to detect specific changes in OTU abundance and community composition during illness. We defined the common core microbiota by varying occurrence and abundance thresholds showing that individual core microbiomes share a substantial number of OTUs across participants, chiefly Streptococci and Veillonella. Our results provide insights into the microbial communities that characterize the healthy human oropharynx, community structure and variability, and provide new approaches to define individual and shared cores. The wider implications of this result include the potential for modeling the general dynamics of oropharynx microbiota both in health and in response to antimicrobial treatments or probiotics.

scholarly journals Elevational changes in bacterial microbiota structure and diversity in an arthropod-disease vector

2021 ◽  
Author(s):  
Tuomas Aivelo ◽  
Mélissa Lemoine ◽  
Barbara Tschirren
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Community Composition ◽  
Vector Competence ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Swiss Alps ◽  
Elevational Gradients ◽  
Disease Vector ◽  
Bacterial Microbiota

Environmental conditions change rapidly along elevational gradients and have been found to affect community composition in macroscopic taxa, with lower diversity typically observed at higher elevations. In contrast, microbial community responses to elevation are still poorly understood. Specifically, the effects of elevation on vector-associated microbiota have not been studied to date, even though the within-vector microbial community is known to influence vector competence for a range of zoonotic pathogens. Here we characterize the structure and diversity of the bacterial microbiota in an important zoonotic disease vector, the sheep tick Ixodes ricinus, along replicated elevational gradient (630 - 1673 masl) in the Swiss Alps. 16S rRNA sequencing of the whole within-tick bacterial microbiota of questing nymphs and adults revealed a decrease in Faith's phylogenetic microbial alpha diversity with increasing elevation, while beta diversity analyses revealed a lower variation in microbial community composition at higher elevations. We also found a higher microbial diversity later in the season and significant differences in microbial diversity among tick life stages and sexes, with lowest microbial alpha diversity observed in adult females. No associations between tick genetic diversity and bacterial diversity were observed. Our study demonstrates systematic changes in tick bacterial microbiota diversity along elevational gradients. The observed patterns mirror diversity changes along elevational gradients typically observed in macroscopic taxa, and they highlight the key role of environmental factors in shaping within-host microbial communities in ectotherms.

scholarly journals Consistent patterns in 16S and 18S microbial diversity from the shells of the common and widespread red-eared slider turtle (Trachemys scripta)

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244489
Author(s):  
Matthew Parks ◽  
Cameron Kedy ◽  
Casey Skalla
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Environmental Samples ◽  
Wildlife Conservation ◽  
Sampling Site ◽  
Alpha Diversity ◽  
Trachemys Scripta ◽  
Freshwater Turtle ◽  
External Shell ◽  
Drying Behavior

Microbial communities associated with freshwater aquatic habitats and resident species are both critical to and indicative of ecosystem status and organismal health. External surfaces of turtle shells readily accumulate microbial growth and could carry representation of habitat-wide microbial diversity, since they are in regular contact with multiple elements of freshwater environments. Yet, microbial diversity residing on freshwater turtle shells is poorly understood. We applied 16S and 18S metabarcoding to characterize microbiota associated with external shell surfaces of 20 red-eared slider (Trachemys scripta) turtles collected from varied habitats in central and western Oklahoma, and ranging to southeast Iowa. Shell-associated microbial communities were highly diverse, with samples dominated by Bacteroidia and alpha-/gamma-proteobacteria, and ciliophoran alveolates. Alpha diversity was lower on turtle shells compared to shallow-water-associated environmental samples, likely resulting from basking-drying behavior and seasonal scute shedding, while alpha diversity was higher on carapace than plastron surfaces. Beta diversity of turtle shells was similarly differentiated from environmental samples, although sampling site was consistently a significant factor. Deinococcus-Thermus bacteria and ciliophoran alveolates were recovered with significantly higher abundance on turtle shells versus environmental samples, while bacterial taxa known to include human-pathogenic species were variably more abundant between shell and environmental samples. Microbial communities from a single, shared-site collection of the ecologically similar river cooter (P. concinna) largely overlapped with those of T. scripta. These data add to a foundation for further characterization of turtle shell microbial communities across species and habitats, with implications for freshwater habitat assessment, microbial ecology and wildlife conservation efforts.

Assessment of bacterial community composition within and among Acropora loripes colonies in the wild and in captivity

Coral Reefs ◽  
2020 ◽  
Vol 39 (5) ◽  
pp. 1245-1255
Author(s):  
Katarina Damjanovic ◽  
Linda L. Blackall ◽  
Lesa M. Peplow ◽  
Madeleine J. H. van Oppen
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
In Captivity ◽  
In The Wild

scholarly journals Effects of Captivity on the Morphology of the Insertion Sites of the Palmar Radiocarpal Ligaments in Hominoid Primates

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1856
Author(s):  
Aroa Casado ◽  
Yasmina Avià ◽  
Miquel Llorente ◽  
David Riba ◽  
Juan Francisco Pastor ◽  
...  
Keyword(s):  
Morphological Characteristics ◽  
Well Being ◽  
Natural Environments ◽  
Habitat Conditions ◽  
Anatomical Changes ◽  
Different Types ◽  
In Captivity ◽  
In The Wild ◽  
Insertion Sites ◽  
The Impact

The environmental conditions of captive hominoid primates can lead to modifications in several aspects of their behavior, including locomotion, which can then alter the morphological characteristics of certain anatomical regions, such as the knee or wrist. We have performed tridimensional geometric morphometrics (3D GM) analyses of the distal radial epiphysis in wild and captive gorillas, chimpanzees, and orangutans. Our objective was to study the morphology of the insertion sites of the palmar radiocarpal ligaments, since the anatomical characteristics of these insertion sites are closely related to the different types of locomotion of these hominoid primates. We have identified significant differences between the wild and captive specimens that are likely related to their different types of locomotion. Our results indicate that the habitat conditions of captive hominoid primates may cause them to modify their locomotor behavior, leading to a greater use of certain movements in captivity than in the wild and resulting in the anatomical changes we have observed. We suggest that creating more natural environments in zoological facilities could reduce the impact of these differences and also increase the well-being of primates raised in captive environments.

scholarly journals Soil microbial community composition in a paddy field with different fertilization managements

2021 ◽  
pp. 1-11
Author(s):  
Limin Wang ◽  
Dongfeng Huang
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Soil Properties ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Phosphorus Fertilization ◽  
Bacterial Phyla ◽  
P Fertilizer

Microbes play vital roles in soil quality; however, their response to N (nitrogen) and P (phosphorus) fertilization in acidic paddy soils of subtropical China remains poorly understood. Here, a 10-year field experiment was conducted to evaluate the effects of different fertilization treatments on microbial communities by Illumina MiSeq sequencing. The results showed that different fertilization treatments did not exert a significant effect on microbial alpha diversity, but altered soil properties, and thus affected microbial community composition. The microbial communities in the T1 (optimized N and P fertilizer) and T2 (excessive N fertilizer) treated soils differed from those in the T0 (no N and P fertilizer) and T3 (excessive P fertilizer) treated soils. In addition, the bacterial phyla Proteobacteria, Chloroflexi, and Acidobacteria, and the fungal phyla Ascomycota and Basidiomycota dominated all the fertilized treatments. Soil total potassium (TK) concentration was the most important factor driving the variation in bacterial community structure under different fertilization regimes, while the major factors shaping fungal community structure were soil TN and NO3–-N (nitrate N). These findings indicate that optimization of N and P application rates might result in variations in soil properties, which changed the microbial community structure in the present study.

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