Disentangling the mechanisms shaping the surface ocean microbiota

Logares, Ramiro; Deutschmann, Ina Maria; Junger, Pedro C.; Giner, Caterina R.; Krabberød, Anders K.; Schmidt, Thomas Sebastian Benedikt; Rubinat-Ripoll, Laura; Mestre, Mireia; Salazar, Guillem; Ruiz‐González, Clara; Sebastián, Marta; Vargas, Colomban de; Acinas, Silvia G.; Duarte, Carlos M.; Gasol, Josep M.; Massana, Ramón

doi:10.1186/s40168-020-00827-8

Cited by 193 publications

(238 citation statements)

References 111 publications

(155 reference statements)

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“…Slight shifts in immune function were found to impact the respiratory microbial communities and they may have been at play here. The strong variation in intra-core zOTUs within individuals highlights that the lung microbiota of dolphins is dynamic and there are likely internal physiological as well as external factors such as temperature [48] involved that impact the bacterial communities on a day-to-day basis.…”

Section: Discussionmentioning

confidence: 99%

Highly abundant core taxa in the blow within and across captive bottlenose dolphins provide evidence for a temporally stable airway microbiota

et al. 2021

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Background The analysis of blow microbiota has been proposed as a biomarker for respiratory health analysis in cetaceans. Yet, we lack crucial knowledge on the long-term stability of the blow microbiota and its potential changes during disease. Research in humans and mice have provided evidence that respiratory disease is accompanied by a shift in microbial communities of the airways. We investigate here the stability of the community composition of the blow microbiota for 13 captive bottlenose dolphins over eight months including both sick and healthy individuals. We used barcoded tag sequencing of the bacterial 16S rRNA gene. Four of the dolphins experienced distinct medical conditions and received systemic antimicrobial treatment during the study. Results We showed that each dolphin harboured a unique community of zero-radius operational taxonomic units (zOTUs) that was present throughout the entire sampling period (‘intra-core’). Although for most dolphins there was significant variation over time, overall the intra-core accounted for an average of 73% of relative abundance of the blow microbiota. In addition, the dolphins shared between 8 and 66 zOTUs on any of the sampling occasions (‘inter-core’), accounting for a relative abundance between 17 and 41% of any dolphin’s airway microbiota. The majority of the intra-core and all of the inter-core zOTUs in this study are commonly found in captive and free-ranging dolphins and have previously been reported from several different body sites. While we did not find a clear effect of microbial treatment on blow microbiota, age and sex of the dolphins did have such an effect. Conclusions The airways of dolphins were colonized by an individual intra-core ‘signature’ that varied in abundance relative to more temporary bacteria. We speculate that the intra-core bacteria interact with the immune response of the respiratory tract and support its function. This study provides the first evidence of individual-specific airway microbiota in cetaceans that is stable over eight months.

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Section: Discussionmentioning

confidence: 99%

Highly abundant core taxa in the blow within and across captive bottlenose dolphins provide evidence for a temporally stable airway microbiota

et al. 2021

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“…recently(Liu et al, 2020;Logares et al, 2020;Stegen et al, 2013;Vass et al, 2020;Yan et al, 2017). For example, studies in lakes found that deterministic processes govern the structure of bacterial communities at different temporal scales (Kent, Yannarell, Rusak, F I G U R E 4 (a) Temporal changes in bacterial relative abundance in Gossenköllesee (GKS) and in Piburgersee (PIB).…”

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confidence: 99%

The balance between deterministic and stochastic processes in structuring lake bacterioplankton community over time

Aguilar

Sommaruga

2020

Molecular Ecology

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One major goal in microbial ecology is to establish the importance of deterministic and stochastic processes for community assembly. This is relevant to explain and predict how diversity changes at different temporal scales. However, understanding of the relative quantitative contribution of these processes and particularly of how they may change over time is limited. Here, we assessed the importance of deterministic and stochastic processes based on the analysis of the bacterial microbiome in one alpine oligotrophic and in one subalpine mesotrophic lake, which were sampled over two consecutive years at different time scales. We found that in both lakes, homogeneous selection (i.e., a deterministic process) was the main assembly process at the annual scale and explained 66.7% of the bacterial community turnover, despite differences in diversity and temporal variability patterns between ecosystems. However, in the alpine lake, homogenizing dispersal (i.e., a stochastic process) was the most important assembly process at the short‐term (daily and weekly) sampling scale and explained 55% of the community turnover. Alpha diversity differed between lakes, and seasonal stability of the bacterial community was more evident in the oligotrophic lake than in the mesotrophic one. Our results demonstrate how important forces that govern temporal changes in bacterial communities act at different time scales. Overall, our study validates on a quantitative basis, the importance and dominance of deterministic processes in structuring bacterial communities in freshwater environments over long time scales.

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“…In the last few years, the study of community assembly in natural ecosystems has shifted its focus from a descriptive “who is there?” approach, to elucidating the relative contribution of stochastic vs. deterministic processes on community assembly (e.g. [97] , [98] , [99] ). Both approaches are indeed pertinent to increase our understanding of the particular ecosystem under investigation.…”

Section: Experimental Systemsmentioning

confidence: 99%

“…In addition to the more common β-diversity analyses, they used null model analysis, neutral models, and co-occurrence networks to assess the relative importance of community assembly processes in soils linked to measured abiotic environments and geographic patterns. Following similar goals and overall analytical framework, Logares and co-workers [99] assessed the drivers of prokaryotic and picoeukaryotic community structure in the sunlit ocean.…”

Section: Representative Studiesmentioning

confidence: 99%

Experimental and computational approaches to unravel microbial community assembly

Cárcer

2020

Computational and Structural Biotechnology Journal

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Microbial communities have a preponderant role in the life support processes of our common home planet Earth. These extremely diverse communities drive global biogeochemical cycles, and develop intimate relationships with most multicellular organisms, with a significant impact on their fitness. Our understanding of their composition and function has enjoyed a significant thrust during the last decade thanks to the rise of high-throughput sequencing technologies. Intriguingly, the diversity patterns observed in nature point to the possible existence of fundamental community assembly rules. Unfortunately, these rules are still poorly understood, despite the fact that their knowledge could spur a scientific, technological, and economic revolution, impacting, for instance, agricultural, environmental, and health-related practices. In this minireview, I recapitulate the most important wet lab techniques and computational approaches currently employed in the study of microbial community assembly, and briefly discuss various experimental designs. Most of these approaches and considerations are also relevant to the study of microbial microevolution, as it has been shown that it can occur in ecological relevant timescales. Moreover, I provide a succinct review of various recent studies, chosen based on the diversity of ecological concepts addressed, experimental designs, and choice of wet lab and computational techniques. This piece aims to serve as a primer to those new to the field, as well as a source of new ideas to the more experienced researchers.

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Disentangling the mechanisms shaping the surface ocean microbiota

Cited by 193 publications

References 111 publications

Highly abundant core taxa in the blow within and across captive bottlenose dolphins provide evidence for a temporally stable airway microbiota

Highly abundant core taxa in the blow within and across captive bottlenose dolphins provide evidence for a temporally stable airway microbiota

The balance between deterministic and stochastic processes in structuring lake bacterioplankton community over time

Experimental and computational approaches to unravel microbial community assembly

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