Microbial Functional Diversity Correlates with Species Diversity along a Temperature Gradient

Ruhl, Ilona A.; Sheremet, Andriy; Smirnova, Angela V.; Sharp, Christine E.; Grasby, Stephen E.; Strous, Marc; Dunfield, Peter F.

doi:10.1128/msystems.00991-21

Cited by 30 publications

(15 citation statements)

References 65 publications

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“…Though the functional categories are different to those in FAPROTAX, both approaches suggest the potential of the midgut bacterial community to perform carbon, nitrogen, and energy metabolism. Consistently with other models [ 102 , 103 ], we observed that the functional trait abundances of the bacterial communities reflect the overall beta diversity, as samples cluster predominantly in a by-tissue pattern ( Fig 8 ). We detected a significant difference in methanol oxidation potential between the crop and midgut.…”

Section: Discussionsupporting

confidence: 90%

Bacterial communities of Aedes aegypti mosquitoes differ between crop and midgut tissues

et al. 2023

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Microbiota studies of Aedes aegypti and other mosquitoes generally focus on the bacterial communities found in adult female midguts. However, other compartments of the digestive tract maintain communities of bacteria which remain almost entirely unstudied. For example, the Dipteran crop is a food storage organ, but few studies have looked at the microbiome of crops in mosquitoes, and only a single previous study has investigated the crop in Ae. aegypti. In this study, we used both culture-dependent and culture-independent methods to compare the bacterial communities in midguts and crops of laboratory reared Ae. aegypti. Both methods revealed a trend towards higher abundance, but also higher variability, of bacteria in the midgut than the crop. When present, bacteria from the genus Elizabethkingia (family Weeksellaceae) dominated midgut bacterial communities. In crops, we found a higher diversity of bacteria, and these communities were generally dominated by acetic acid bacteria (family Acetobacteriaceae) from the genera Tanticharoenia and Asaia. These three taxa drove significant community structure differences between the tissues. We used FAPROTAX to predict the metabolic functions of these communities and found that crop bacterial communities were significantly more likely to contain bacteria capable of methanol oxidation and methylotrophy. Both the presence of acetic acid bacteria (which commonly catabolize sugar to produce acetic acid) and the functional profile that includes methanol oxidation (which is correlated with bacteria found with natural sources like nectar) may relate to the presence of sugar, which is stored in the mosquito crop. A better understanding of what bacteria are present in the digestive tract of mosquitoes and how these communities assemble will inform how the microbiota impacts mosquito physiology and the full spectrum of functions provided by the microbiota. It may also facilitate better methods of engineering the mosquito microbiome for vector control or prevention of disease transmission.

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Section: Discussionsupporting

confidence: 90%

Bacterial communities of Aedes aegypti mosquitoes differ between crop and midgut tissues

et al. 2023

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show abstract

“…Though the functional categories are different to those in FAPROTAX, both approaches suggest the potential of the midgut bacterial community to perform carbon, nitrogen, and energy metabolism. Consistently with other models [99,100], we observed how the functional trait abundances of the bacterial communities reflect the overall beta diversity, as samples cluster predominantly in a by-tissue pattern. We detected a significant difference in methanol oxidation potential between the crop and midgut.…”

Section: Discussionsupporting

confidence: 90%

Bacterial communities of Aedes aegypti mosquitoes differ between crop and midgut tissues

Villegas

Radl

Dimopoulos

et al. 2022

Preprint

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Microbiota studies of Aedes aegypti and other mosquitoes generally focus on the bacterial communities found in adult female midguts. However, other compartments of the digestive tract maintain communities of bacteria which remain almost entirely unstudied. For example, the Dipteran crop stores nectar and other sugars, but few studies have looked at the microbiome of crops in mosquitoes, and only a single previous study has investigated the crop in Ae. aegypti. In this study, we used both culture-dependent and culture-independent methods to compare the bacterial communities in midguts and crops of laboratory-reared Ae. aegypti. Both methods revealed a trend towards higher abundance, but also higher variability, of bacteria in the midgut than the crop. When present, bacteria from the genus Elizabethkingia (family Weeksellaceae) dominated midgut bacterial communities. In crops, we found a higher diversity of bacteria, and these communities were generally dominated by acetic acid bacteria (family Acetobacteriaceae) from the genera Tanticharoenia and Asaia. These three taxa drove significant community structure differences between the tissues. We used FAPROTAX to predict the metabolic functions of these communities and found that crop bacterial communities were significantly more likely to contain bacteria capable of methanol oxidation and methylotrophy. Both the presence of acetic acid bacteria (which commonly catabolize sugar to produce acetic acid) and the functional profile that includes methanol oxidation (which is correlated with bacteria found with natural sources like nectar) may relate to the presence of sugar in the crop. A better understanding of what bacteria are present in the digestive tract of mosquitoes and how these communities assemble will inform how the microbiota impacts mosquito physiology and the full spectrum of functions provided by the microbiota. It may also facilitate better methods of engineering the mosquito microbiome for vector control or prevention of disease transmission.

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“…This tendency is also indicated in Fig. S3 of Ruhl et al 2022, where log-transformed data, being less dense with smaller TR levels, leads to overestimation. As our focus is on the initial phases of microbial extinctions and their impacts on ecosystem multifunctionality, the bias introduced by severe extinctions (e.g., 95% reduction of the maximum ASV richness) does not significantly compromise the efficacy of the power-law regression method for assessing multifunctional redundancy.…”

Section: Setting For Asv-extinction Simulations and Fitting Of Power-...supporting

confidence: 57%

“…Second, the comparison of redundancy exponents between this study and past studies (21,29) provides insights into the robustness of the proposed method and offers cautions for its application to other systems. The exponent (a) values estimated in Miki, Yokokawa and Matsui (2014) ranged from 0.55 to 0.75, but these may have been overestimated as they were derived from pseudo-communities containing a single strain from each genus.…”

Section: Advancing Methodology: Underexplored Aspects and Future Dire...mentioning

confidence: 82%

Advancing marker-gene-based methods for prokaryote-mediated multifunctional redundancy: exploring random and nonrandom extinctions in a watershed

Cheng,

Miki,

Ido

et al. 2024

Preprint

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Multifunctional redundancy, the extent of loss in multiple ecosystem functions with decreasing biodiversity, stands as a crucial index for evaluating ecosystem resilience to environmental changes. We aimed to refine a marker-gene-based methodology for quantifying multifunctional redundancy in prokaryotic communities. Using PICRUSt2, we predicted KEGG orthologs (KOs) for each Amplicon Sequence Variant (ASV), assessed community-wide KO richness, and validated predictions against experimentally quantified phenotypic multifunctionality. Additionally, we introduced a refined regression on ASV richness–KO richness curves, providing a reliable estimate of the power-law exponent within computational time constraints, serving as the multifunctional redundancy index. Incorporating various non-random extinction scenarios alongside a random one allowed us to quantify estimate variations between scenarios, providing conservative estimates of multifunctional redundancy. Applied to Lake Biwa and four of its inlet rivers, the refined methodology unveiled spatio-temporal variations in multifunctional redundancy. Our analysis demonstrated lower redundancy in Lake Biwa compared to rivers, aiding in prioritizing conservation targets and inferring distinct community assembly processes. Future directions include a deeper exploration of KO composition information for detailed multifunctionality quantification and the refinement of extinction scenarios. This study demonstrates the promising integration of bioinformatic functional prediction and modeling biodiversity loss, offering a valuable tool for effective ecosystem management.

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Microbial Functional Diversity Correlates with Species Diversity along a Temperature Gradient

Cited by 30 publications

References 65 publications

Bacterial communities of Aedes aegypti mosquitoes differ between crop and midgut tissues

Bacterial communities of Aedes aegypti mosquitoes differ between crop and midgut tissues

Bacterial communities of Aedes aegypti mosquitoes differ between crop and midgut tissues

Advancing marker-gene-based methods for prokaryote-mediated multifunctional redundancy: exploring random and nonrandom extinctions in a watershed

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