Biology subjects

Sikorski, J.

Publications and source records attributed to Sikorski, J..

3 recordsLinked to original sources

bioRxiv2024

Succession of bacteria and archaea within the soil micro-food web

Bacterivorous nematodes represent numerically abundant bacterial grazers in the soil micro-food web. Their trophic regulation shapes the soil microbiome, but the underlying population dynamics of bacteria and archaea are poorly understood. Here, we followed bulk soil respiration and time-resolved population dynamics (32 days) of bacterial and archaeal species in response to top-down control by a common bacterivorous soil nematode, Acrobeloides buetschlii, bottom-up control by resource amendment via maize litter as well as the combination of both. Addition of maize litter significantly increased soil respiration rates, while bacterivorous nematodes shifted the maximum rate of soil respiration from day 12 to day 6. Underlying bacterial and archaeal abundance changes could be separated into five major response types, dominating in different top-down and bottom-up control scenarios. Individual microbial species switched between response types depending on the different scenarios. In-depth analysis of these differential abundance patterns revealed a broad feeding behavior for A. buetschlii on dominating populations of gram-negative bacteria (Acidobacteriota, Bacteroidota, Gemmatimonatoda, Pseudomonadota) and ammonia-oxidizing archaea (Nitrososphaerota), while discriminating against dominant populations of gram-positive bacteria (Actinobacteriota, Bacillota). Combined bottom-up control by maize litter and top-down control by nematode grazing caused a succession of soil microbiota, which was driven by population changes first in the Bacteroidota, then in the Pseudomonadota, and last in the Acidobacteriota and Nitrososphaerota. This mechanistic understanding of nematode grazing on soil microbiota population dynamics is essential to inform predictive models of the soil food web.

microbiology↗

bioRxiv2024

Old, deciduous stands support both high biodiversity and carbon storage in German forests

Ecosystems worldwide face threats related to human-driven degradation, climate change, and biodiversity loss. Addressing these challenges requires management strategies that combine biodiversity conservation with climate change mitigation. Here, we aimed to identify local-scale management actions that promote biodiversity at multiple trophic levels while also promoting carbon storage and sequestration. We combined data on the diversity of nine taxonomic groups (plants, birds, moths, Mollusca, soil fungi, active soil bacteria, Cercozoan and Endomyxan soil protists, Oomycotan soil protists, and nematodes), with above- and belowground carbon storage in 150 temperate forest plots in three regions of Germany. These were dominated by European beech, pine, spruce and oak. We investigated the relationships between multiple forest structure and management variables, biodiversity and carbon storage and sequestration in forest plots with different management types. Carbon storage was 32% higher in uneven-aged than even-aged forests and increased with mean tree diameter, while carbon sequestration in trees was 15% higher in even-aged than uneven-aged stands. Mean tree diameter was positively related to overall biodiversity, especially bird species richness and the richness of forest specialist birds. Oak and beech-dominated stands harboured higher biodiversity than stands dominated by conifers (especially Pine). One exception to this was the richness of plant species and forest specialist plants, which were highest in spruce plantations. Surprisingly, deadwood input did not significantly affect the diversity of any taxonomic group in this study. By showing that older forests with a high proportion of uneven-aged broad-leafed trees, or oak-dominated forests, can promote both biodiversity and carbon storage, our results could help inform sustainable local-scale forest management in Central Europe that promotes both biodiversity conservation and carbon storage. These findings can form the basis of further larger-scale studies investigating such relations at larger spatial scales to inform landscape-level recommendations for sustainable multifunctional forest management.

ecology↗

bioRxiv2019

Phylogenomic analysis reveals the basis of adaptation of Pseudorhizobium species to extreme environments

The family Rhizobiaceae includes many genera of soil bacteria, often isolated for their association with plants. Herein, we investigate the genomic diversity of a group of Rhizobium species and unclassified strains isolated from atypical environments, including seawater, rock matrix or polluted soil. Based on whole-genome similarity and core genome phylogeny, we show that this group corresponds to the genus Pseudorhizobium. We thus reclassify Rhizobium halotolerans, R. marinum, R. flavum and R. endolithicum as P. halotolerans comb. nov., P. marinum comb. nov., P. flavum comb. nov. and R. endolithicum comb. nov., respectively, and show that P. pelagicum is a synonym of P. marinum. We also delineate a new chemolithoautotroph species, P. banfieldiae sp. nov., whose type strain is NT-26T (= DSM 106348T = CFBP 8663T). This genome-based classification was supported by a chemotaxonomic comparison, with gradual taxonomic resolution provided by fatty acid, protein and metabolic profiles. In addition, we used a phylogenetic approach to infer scenarios of duplication, horizontal transfer and loss for all genes in the Pseudorhizobium pangenome. We thus identify the key functions associated with the diversification of each species and higher clades, shedding light on the mechanisms of adaptation to their respective ecological niches. Respiratory proteins acquired at the origin of Pseudorhizobium are combined with clade-specific genes to encode different strategies for detoxification and nutrition in harsh, nutrient-poor environments. Finally, we predict diagnostic phenotypes for the distinction of P. banfieldiae from other Pseudorhizobium species, including autotrophy and sensitivity to the azo dye Congo Red, which we experimentally validated.

microbiology↗