The fabric of sedimentary rocks in lacustrine archives usually contains long and continuous proxy records of biological, chemical and physical parameters that can be used to study past environmental and climatic variability. Here we propose an innovative approach to sedimentary facies analysis based on a coupled geomicrobiological and sedimentological study using high-resolution microscopic techniques in combination with mineralogical analyses. We test the applicability of this approach on Lake Son Kul, a high alpine lake in central Tien Shan (Kyrgyzstan) by looking at the mineral fabric and microbial communities observed down to the nanoscale. The characterization of microbe–mineral interactions allows the origin of four carbonate minerals (e.g. aragonite, dolomite, Mg-calcite, calcite) to be determined as primary or diagenetic phases in Lake Son Kul. Aragonite was mainly of primary origin and is driven by biological activity in the epilimnion, whereas diagenetic minerals such as Mg-calcite, calcite, dolomite and pyrite were triggered by bacterial sulphate reduction and possibly by methanotrophic archaea. A new morphotype of aragonite (i.e. spherulite-like precursor) occurs in Unit IV (c. 7100–5000 cal. BP) associated with microbial mat structures. The latter enhanced the preservation of viral relics, which have not yet been reported in Holocene lacustrine sediments. This study advocates that microbe–mineral interactions screened down to the nanoscale (e.g. virus-like particles) can be used successfully for a comprehensive description of the fabric of laminated lake sediments. In this sense, they complement traditional facies sedimentology tools and offer valuable new insights into: (1) the study of microbial and viral biosignatures in Quaternary sediments; and (2) palaeoenvironmental reconstructions.

Virus-like particles were observed in thin sections of partially bleaching colonies of the scleractinian Acropora cytherea, collected in the Hon Mun Marine Protected Area (Vietnam). The most common particles were found in the cytoplasm of epidermal cells, exhibiting icosahedral symmetry and measuring 90–140 nm in diameter. Some had a tail-like structure resembling that of certain Hepadnaviridae such as the hepatitis B virus. Some others were tailless with a virion size. Overall, less than 10% of the cells showed obvious signs of infection. Images of virally-parasitized tissues of A. cytherea provide further evidence that corals are a target for viral infection. However, more research is required into their pathogenicity and involvement in bleaching events.

The Eucoilid parasitoid Leptopilina boulardi is able to suppress its host Drosophila melanogaster immune reaction. Some strains, however, are non-immune suppressive to that host. Virus-like particles (VLPs) responsible for the immune suppressive ability were investigated in different strains of L, boulardi with histochemical and ultrastructural techniques. Membrane-bound particles containing vesicles were observed in the reservoir of the long gland and also in the egg canal of the ovipositor. These particles are homologous with the immune suppressive VLPs already described in the reservoir of L. heterotoma. Similarities were also observed with the L2 particles described previously around the chorion of the parasitoid egg after infestation. A weak positive DNA specific histochemical reaction was observed inside the reservoir and at the ultrastructural level. Feulgen-derived techniques demonstrated that the reaction was localized inside the particles. The morphology of the particles as well as the immune suppressive ability varied between strains. Two morphotypes of VLPs are described; the ‘Is’ morphotype (always observed in immune suppressive or Is strains) and the ‘NIs’ morphotype (observed in the non-immune suppressive or NIs strain). The hybrids between Is and NIs strains produce a third type of particle, the ‘His’morphotype with half-immune suppressive ability and intermediate morphology. The origin of the particles' immune suppressive activity against D. melanogaster is discussed within the scope of host specificity.

Teneral nulliparous tsetse Glossina pallidipes were infected with virus-like particles by two pathways: haemocoelic microinjection, and oral feeding with a micropipette. Samples of tsetse were dissected every 3 days; and at 22 days post-infection, cumulative per cent infection was 44.4 and 31.3% for microinjection and per os infection, respectively. Natural virus-like particle infection in the population was 3.6%. Thus the infectious nature of virus-like particles was established, together with two possible pathways of infection.