Mass collection of magnetotactic bacteria from the permanently stratified ferruginous Lake Pavin, France

Abstract

Obtaining high biomass yields of specific microorganisms for culture-independent approaches is a challenge faced by scientists studying organisms recalcitrant to laboratory conditions and culture. This difficulty is highly decreased when studying magnetotactic bacteria (MTB) since their unique behavior allows their enrichment and purification from other microorganisms present in aquatic environments. Here, we use Lake Pavin, a permanently stratified lake in the French Massif Central, as a natural laboratory to optimize collection and concentration of MTB that thrive in the water column and sediments. A method is presented to separate MTB from highly abundant abiotic magnetic particles in the sediment of this crater lake. For the water column, different sampling approaches are compared such as in situ collection using a Niskin bottle and online pumping. By monitoring several physicochemical parameters of the water column, we identify the ecological niche where MTB live. Then, by focusing our sampling at the peak of MTB abundance, we show that the online pumping system is the most efficient for fast recovering of large volumes of water at a high spatial resolution, which is necessary considering the sharp physicochemical gradients observed in the water column. Taking advantage of aerotactic and magnetic MTB properties, we present an efficient method for MTB concentration from large volumes of water. Our methodology represents a first step for further multidisciplinary investigations of the diversity, metagenomic and ecology of MTB populations in Lake Pavin and elsewhere, as well as chemical and isotopic analyses of their magnetosomes.

Biogeochemical Niche of Magnetotactic Cocci Capable of Sequestering Large Polyphosphate Inclusions in the Anoxic Layer of the Lake Pavin Water Column

“…The physicochemical profile acquired on the first day in Lake Pavin allowed us to localise the OATZ and MTB communities in the water column ( Figure 1 ). In detail, the oxygen concentration of the water column underwent a steep decrease around the 49.7-m depth from ∼40% down to the probe detection limit and complete anoxia at around 50.3 m. In line with previous observations ( Busigny et al, 2021 ), specific conductivity, dissolved organic matter concentration, and temperature gradually increased with depth from ∼60 to >200 μS cm –1 , from 1 to 5 relative fluorescence units, and from 4°C to >4.5°C, respectively. Moreover, a typical small turbidity peak was observed at a depth just below oxygen disappearance.…”

“…The water column of the ferruginous meromictic Lake Pavin, France (45.495792°N, 2.888117°E), was sampled in October 2019 from a platform anchored at its centre where the lake is the deepest (∼90 m). Previous campaigns showed that MTB are found under the OATZ at depths where dioxygen becomes undetectable and in a specific range of conductivity ( Busigny et al, 2021 ). The vertical localisation of this zone varied slightly over the seasons due to lake dynamics.…”

“…When reaching 50.7 m (i.e., depth close to the one of first MTB appearance on the 1st day), 9 samples vertically spaced by ∼20 cm on average were collected and further used to determine the MTB cell concentration, diversity, and physicochemical features. Samples were collected using a flexible metered hose following the same protocol as that of Busigny et al (2021) . The ∼65-m-long hose was connected at its near-surface end to a speed-adjustable 12-V brushless pump (DC50E-1250A).…”

“…In the present work, we investigated the depth stratification of the diverse MTB populations in relation to environmental parameters in the water column of Lake Pavin. Using a recently developed methodology coupling in situ measurements and water sampling with a high vertical resolution ( Busigny et al, 2021 ), we localised the depth range in the OATZ where the MTB community thrive. We collected water samples from a transect at the redox boundary with a 20-cm interval and examined the MTB morphotype diversity and abundance using magnetic sorting and light microscopy approaches.…”

Bioinspired Magnetic Nanochains for Medicine

“…One of the reasons may be the challenging separation and harvesting of nanochains from bacteria without structural damage, since the procedure typically requires the use of chemicals (such as surfactants) and mechanical treatments (such as exposure to ultrasonic probes). Indeed, the process can easily be harsh enough to disrupt the fibrillar network that supports the magnetosomes’ chains, as well as, at least partially, destroy the sensitive magnetosome membrane [ 134 , 135 ]. Therefore, as evidenced from the electron microscopy analyses in the majority of publications, the results of nanochain harvesting are usually isolated magnetite nanocrystals rather than intact magnetic nanochains.…”