Could benthic biofilm analyses be used as a reliable proxy for freshwater environmental health?

Pu, Yunfeng; Ngan, Wing Yui; Yao, Yuan; Habimana, Olivier

doi:10.1016/j.envpol.2019.05.111

Cited by 22 publications

(13 citation statements)

References 41 publications

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“…S2, to be a very small water body, which is likely to be easily enriched by runoff. As Further, it is in line with the notion that sporadic pollution events of aquatic environments cannot always be detected by bulk water monitoring strategies, while biofilms do capture such events and bear testament to them [47].…”

Section: Anthropogenic Eutrophication Promotes Skin Dysbiosissupporting

confidence: 79%

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system

Krotman

Yergaliyev

Alexander

et al. 2019

Preprint

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Fish skin microbiomes are rarely studied in inland water systems, in spite of their importance for fish health and ecology. This is mainly because fish species distribution often covaries with other biotic and abiotic factors, complicating the study-design. We tackled this issue in the northern part of the Jordan River system, in which a few fish species geographically overlap, across a steep gradients of water temperature and salinity. Using 16S rRNA metabarcoding, we studied the water properties that shape the skin bacterial communities, and their interaction with fish taxonomy. We found that considering the skin-community contamination by water microbial community is important, even when the water and skin communities are apparently different. With this in mind, we found alpha diversity of the skin-communities to be stable across sites, but higher in bentic loaches, compared to other fish.Beta diversity was found to be different among sites and to weakly covary with the dissolved oxygen, when treated skin-communities were considered. In contrast, water temperature and conductivity were strong factors explaining beta diversity in the untreated skin-communities. Beta diversity differences between co-occurring fish species emerged only for the treated skin-communities.Metagenomics predictions highlighted the microbiome functional implications of excluding the watercommunities contamination from the fish skin-communities. Finally, we found that human induced eutrophication promotes dysbiosis of the fish skin-community, with signatures relating to fish health. This finding was in line with recent studies, showing that biofilms capture sporadic pollution events, undetectable by interspersed water monitoring.

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Section: Anthropogenic Eutrophication Promotes Skin Dysbiosissupporting

confidence: 79%

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system

Krotman

Yergaliyev

Alexander

et al. 2019

Preprint

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show abstract

“…This result supports the finding of Legrand et al [46] as a useful ecological bioindicator for monitoring wild environments. Further, it is in line with the notion that sporadic pollution events of aquatic environments cannot always be detected by bulk water monitoring strategies, while biofilms do capture such events and bear testament to them [49].…”

Section: Anthropogenic Eutrophication Promotes Skin Dysbiosissupporting

confidence: 77%

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system

Krotman¹,

Yergaliyev

Shani

et al. 2020

Microbiome

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Background: Fish skin microbiomes are rarely studied in inland water systems, in spite of their importance for fish health and ecology. This is mainly because fish species distribution often covaries with other biotic and abiotic factors, complicating the study design. We tackled this issue in the northern part of the Jordan River system, in which a few fish species geographically overlap, across steep gradients of water temperature and salinity. Results: Using 16S rRNA metabarcoding, we studied the water properties that shape the skin bacterial communities, and their interaction with fish taxonomy. To better characterise the indigenous skin community, we excluded bacteria that were equally abundant in the skin samples and in the water samples, from our analysis of the skin samples. With this in mind, we found alpha diversity of the skin communities to be stable across sites, but higher in benthic loaches, compared to other fish. Beta diversity was found to be different among sites and to weakly covary with the dissolved oxygen, when treated skin communities were considered. In contrast, water temperature and conductivity were strong factors explaining beta diversity in the untreated skin communities. Beta diversity differences between co-occurring fish species emerged only for the treated skin communities. Metagenomics predictions highlighted the microbiome functional implications of excluding the water community contamination from the fish skin communities. Finally, we found that human-induced eutrophication promotes dysbiosis of the fish skin community, with signatures relating to fish health. Conclusions: Consideration of the background water microbiome when studying fish skin microbiomes, across varying fish species and water properties, exposes patterns otherwise undetected and highlight among-fish-species differences. We suggest that sporadic nutrient pollution events, otherwise undetected, drive fish skin communities to dysbiosis. This finding is in line with a recent study, showing that biofilms capture sporadic pollution events, undetectable by interspersed water monitoring.

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“…Two of them, Rhodoferax sp (LN870966) and Undibacterium seohonense (KC735151), also proliferated in GDM biofilms after addition of starch 43 , suggesting that their role as indicators might go beyond a particular lake and carbon source. Metabarcoding of pro- and eukaryotic marker genes from different habitats -including biofilms 53 - is increasingly regarded as a powerful tool for future environmental monitoring 54 , 55 . Recently, Keeley et al reported that a small number of abundant microbial genotypes within operationally defined ‘eco-groups’ could accurately predict the enrichment of benthic habitats in salmon farms 56 .…”

Section: Discussionmentioning

confidence: 99%

Biomass addition alters community assembly in ultrafiltration membrane biofilms

Silva

2020

Sci Rep

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Freshwater biofilms assemble from a pool of rare water column genotypes. Random density fluctuations and temporal species turnover of functionally equivalent potential colonizers result in compositional variability of newly formed biofilm communities. We hypothesized that stronger environmental filtering as induced by enhanced substrate levels might reduce the impact of a locally variable pool of colonizers and instead select for more universal habitat specialists. Our model were heterotrophic biofilms that form on membranes during gravity-driven ultrafiltration of lake water. In four separate experiments, biomass of the cyanobacterium Microcystis was added to the feed water of one set of treatments (BM) and the resulting biofilm communities were compared to unamended controls (CTRL). Biomass addition led to a significant shift of community assembly processes: Replicate BM biofilms were more similar to each other than by chance in 3 of 4 experiments, whereas the opposite was the case for CTRL communities. Moreover, BM communities were more stochastically assembled across experiments from a common ‘regional’ pool of biofilm colonizers, whereas the composition of CTRL communities was mainly determined by experiment-specific ‘local’ genotypes. Interestingly, community assembly processes were also related to both, physiology (aerobic vs. anaerobic lifestyle) and the phylogenetic affiliation of biofilm bacteria.

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Could benthic biofilm analyses be used as a reliable proxy for freshwater environmental health?

Cited by 22 publications

References 41 publications

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system

Biomass addition alters community assembly in ultrafiltration membrane biofilms

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