Aguera, A. | bioRxiv Science

bioRxiv2022

High frequency monitoring of feeding activity in benthic suspension feeders

Suspension feeders ecosystem role and services are mainly driven by their efficiency in clearing particles from the water column. As such there is an interest on suspension feeders feeding activity and how they interact with the ecosystem. Advancing research on feeding response requires experimental designs where individuals can be exposed to continuously changing environments and where feeding activity can be monitored at a high frequency and at different time scales. There are several methods to monitor feeding activity (as clearance rate (CR) and particle capture efficiency (CE)) of suspension feeders. Among them, the flow-through method is most often used and it allows individuals to be exposed to changing conditions. However, as with the other existing methods, the flow-through method is labor intensive and time consuming limiting both the number of individuals that could be observed simultaneously and the resolution at which measurements can be taken. The flow-through method is constrained by the need to measure the flow rate through the chambers and to take samples to determine particle concentration in the water. In this work we automated the standard flow-through method using micro-controller based prototyping. The result is a methodological approach that continuously monitor feeding at high frequency and on a larger number of individuals while reducing handling and measurement errors. This work provides the description and assessment of the automated set-up, which is an end to end solution that can readily assembled and configured.

ecology↗

bioRxiv2020

Nutritional inter-dependencies and a carbazole-dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazol

BackgroundThiabendazole (TBZ), is a benzimidazole fungicide and anthelminthic whose high persistence and toxicity pose a serious environmental threat. In our quest for environmental mitigation we previously isolated the first TBZ-degrading bacterial consortium and provided preliminary evidence for its composition and the degrading role of a Sphingomonas. Here, we employed a multi-omic approach combined with DNA-stable isotope probing (SIP) to determine the genetic make-up of the key consortium members, to disentangle nutritional and metabolic interdependencies, to identify the transformation pathway of TBZ and to understand the genetic network driving its transformation. ResultsTime-series SIP in combination with amplicon sequencing analysis verified the key role of Sphingomonas in TBZ degradation by assimilating over 80% of the 13C-labelled phenyl moiety of TBZ. Non-target mass spectroscopy (MS) analysis showed the accumulation of thiazole-4-carboxamidine as a single dead-end transformation product and no phenyl-containing derivative, in line with the phenyl moiety assimilation in the SIP analysis. Time series metagenomic analysis of the consortium supplemented with TBZ or succinate led to the assembly of 18 metagenome-assembled genomes (MAGs) with >80% completeness, six (Sphingomonas 3X21F,{gamma} -Proteobacterium 34A, Bradyrhizobiaceae 9B and Hydrogenophaga 19A, 13A, and 23F) being dominant. Meta-transcriptomic and -proteomic analysis suggested that Sphingomonas mobilize a carbazole dioxygenase (car) operon during the initial cleavage of TBZ to thiazole-4-carboxamidine and catechol, the latter is further transformed by enzymes encoded in a catechol ortho-cleavage (cat) operon; both operons being up-regulated during TBZ degradation. Computational docking analysis of the terminal oxygenase component of car, CarAa, showed high affinity to TBZ, comparable to carbazole, reinforcing its high potency for TBZ transformation. These results suggest no interactions between consortium members in TBZ transformation, performed solely by Sphingomonas. In contrast, gene expression network analysis revealed strong interactions between Sphingomonas MAG 3X12F and Hydrogenophaga MAG 23F, with Hydrogenophaga activating its cobalamin biosynthetic pathway and Sphingomonas its cobalamin salvage pathway along TBZ degradation. ConclusionsOur findings suggest interactions between consortium members which align with the "black queen hypothesis": Sphingomonas detoxifies TBZ, releasing consortium members by a toxicant; in return for this, Hydrogenophaga 23F provides cobalamin to the auxotrophic Sphingomonas.

systems biology↗