Biology subjects

Smalla, K.

Publications and source records attributed to Smalla, K..

8 recordsLinked to original sources

bioRxiv2026

Antimicrobial resistant bacteria in wastewater-irrigated Mexican soils and transfer of resistant bacteria from irrigated soils to cilantro plants

Agricultural fields in the Mezquital Valley, Mexico, were irrigated with untreated wastewater over several decades. Following the construction of a wastewater treatment plant (WWTP) in Atotonilco de Tula, WWTP effluent is used for irrigation. To evaluate the effects of changed irrigation, a soil incubation experiment was performed. Soils of the Mezquital Valley long-term irrigated with untreated wastewater were irrigated with WWTP influent or effluent, both unspiked and spiked with antibiotics and biocidal compounds and incubated four weeks. We investigated the effects of shifted irrigation on the abundance of cultivable total heterotrophic and resistant bacteria (RB). Additionally, RB were cultivated from Coriandrum sativum (cilantro) sown in soil of the incubation experiment. While wastewater treatment significantly reduced the bacterial abundance in effluent, spiking increased RB abundance in both wastewater types including ciprofloxacin (CIP) RB. Before wastewater addition, all soils contained cultivable RB. Irrigation increased the relative abundance of RB cultivated on Mueller Hinton (MH) agar in Leptosols and Phaeozems, compared to soils prior to wastewater addition irrespective of the water type, but not in Vertisols, suggesting the soil type rather than water qualities influenced the RB abundance. Diverse CIP RB were cultivated including strains of 14 genera of three phyla. Among those, Achromobacter spp. strains related to potentially pathogenic A. spanius originating from soil were abundant in both leaves and roots of cilantro. Our results showed that the implementation of wastewater treatment does not reduce the abundance of cultivable RB in Mezquital Valley soils and cilantro plants. Health risk associated monitoring should include long-term persistent RB colonizing plants cultivated in wastewater irrigated soils.

microbiology↗

bioRxiv2025

Novel insights into the genome organization of Rhizobiaceae: identification of linear plasmids

2.Members of the family Rhizobiaceae typically have multipartite genomes, that are split between two or more replicons, including the chromosome and a variable number of extrachromosomal replicons (chromids and plasmids). Nearly all Rhizobiaceae replicons sequenced and described to date have a circular topology, with the exception of the linear chromid found in the genomes of most Agrobacterium spp. In this study, genomes of five nonpathogenic Agrobacterium strains and one plant tumorigenic Allorhizobium strain were fully sequenced. Surprisingly, genome analysis revealed that these six strains each carry an 80-kbp linear plasmid. Linear plasmids were so far not identified in this bacterial family or other bacteria within the class Alphaproteobacteria. The ends of all six plasmids identified in this study have a hairpin structure with covalently closed ends. The plasmid sequences showed a high degree of homology, clearly indicating their common ancestry. Database searches led to the identification of additional linear plasmids in previously published Rhizobiaceae genome assemblies that were not previously recognized to have linear plasmids, suggesting that these replicons may be more widespread. Most likely, linear plasmids may be even more widely distributed than anticipated. Although the biological functions of the linear plasmids identified in this study remain unknown, they are associated with both nonpathogenic and plant tumorigenic Rhizobiaceae strains. 3. Impact statementThe family Rhizobiaceae includes some remarkable and important representatives, such as plant symbiotic bacteria (rhizobia) and plant pathogenic bacteria associated with neoplasia (agrobacteria). In this study, the complete genome sequences of six Rhizobiaceae strains were generated and their genome organizations were examined. Strikingly, our results showed that these six strains harbor a linear plasmid. Moreover, GenBank searches suggested that linear plasmids may be even more widespread in the family Rhizobiaceae. Linear plasmids may go undetected in genome sequencing studies if the assemblies are not specifically examined for linear plasmid. Overall, this study provides further evidence for the extraordinary genome plasticity of members of the family Rhizobiaceae and expands the taxonomic range in which linear plasmids have been identified. To the best of our knowledge, this is the first report of linear plasmids in the family Rhizobiaceae or the class Alphaproteobacteria. 4. Data summaryThe whole-genome sequences have been deposited at DDBJ/ENA/GenBank under the accessions CP192696-CP192701 (Av2), CP000000-CP000000 (rho-7.1), CP000000-CP000000 (rho-8.1), CP000000-CP000000 (rho-11.1), CP000000-CP000000 (rho-13.3), and CP000000-CP000000 (rho-14.1), within the BioProjects PRJNA557463 and PRJNA1009994. The raw sequencing reads were deposited in the Sequence Read Archive (SRA) under the same BioProjects PRJNA557463 and PRJNA1009994: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA557463 and https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1009994. NCBI submission for five genome sequences is undergoing processing and accession numbers will be added when available; in https://figshare.com/s/29a9e621adc1b66d0957

genomics↗

bioRxiv2023

Heritable maize microbiomes contribute to local adaptation and host stress resilience

Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbe interactions in the face of environmental stress. Here, we surveyed the root and rhizosphere microbiome of 129 accessions of locally adapted Zea mays, sourced from diverse habitats and grown under control and different stress conditions. We quantified treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome composition. Genome wide association analysis identified host genetic variants linked to both rhizosphere microbiome composition and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone microbe Massilia and source total soil nitrogen, finding mutant plants to show a reduction in lateral root density. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress.

genetics↗

bioRxiv2023

Genomics of the "tumorigenes" clade of the family Rhizobiaceae and description of Rhizobium rhododendri sp. nov.

Tumorigenic members of the family Rhizobiaceae, known as agrobacteria, are responsible for crown and cane gall diseases of various agricultural crops worldwide. Tumorigenic agrobacteria are commonly found in the genera Agrobacterium, Allorhizobium, and Rhizobium. In this study, we analyzed a distinct "tumorigenes" clade of the genus Rhizobium, which includes the tumorigenic species Rhizobium tumorigenes, as well as strains causing crown gall disease on rhododendron. Here, high quality, closed genomes of representatives of the "tumorigenes" clade were generated, followed by comparative genomic and phylogenomic analyses. Additionally, phenotypic characteristics of representatives of the "tumorigenes" clade were analyzed. Our results showed that the tumorigenic strains isolated from rhododendron represent a novel species of the genus Rhizobium for which the name Rhizobium rhododendri sp. nov. is proposed. This species also includes additional strains originating from blueberry and Himalayan blackberry in USA, whose genome sequences were retrieved from GenBank. Both R. tumorigenes and R. rhododendri contain multipartite genomes, including a chromosome, putative chromids, and megaplasmids. Synteny and phylogenetic analyses indicated that a large putative chromid of R. rhododendri resulted from the cointegration of an ancestral megaplasmid and two putative chromids, following its divergence from R. tumorigenes. Moreover, gene clusters specific for both species of the "tumorigenes" clade were identified, and their biological functions and roles in ecological diversification of R. rhododendri and R. tumorigenes were predicted and discussed.

microbiology↗

bioRxiv2020

Revisiting the taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis) using genomics - emended description of All. vitis sensu stricto and description of Allorhizobium ampelinum sp. nov.

BackgroundAllorhizobium vitis (formerly named Agrobacterium vitis or Agrobacterium biovar 3) is the primary causative agent of crown gall disease of grapevine worldwide. We obtained and analyzed whole-genome sequences of diverse All. vitis strains to get insights into their diversification and taxonomy. ResultsPairwise genome comparisons and phylogenomic analysis of various All. vitis strains clearly indicated that All. vitis is not a single species, but represents a species complex composed of several genomic species. Thus, we emended the description of All. vitis, which now refers to a restricted group of strains within the All. vitis species complex (i.e. All. vitis sensu stricto) and proposed a description of a novel species, All. ampelinum sp. nov. The type strain of All. vitis sensu stricto remains the current type strain of All. vitis, K309T. The type strain of All. ampelinum sp. nov. is S4T. We also identified sets of gene clusters specific to the All. vitis species complex, All. vitis sensu stricto and All. ampelinum, respectively, for which we predicted the biological function and infer the role in ecological diversification of these clades, including some we could experimentally validate. All. vitis species complex-specific genes confer tolerance to different stresses, including exposure to aromatic compounds. Similarly, All. vitis sensu stricto-specific genes confer the ability to degrade 4-hydroxyphenylacetate and a putative compound related to gentisic acid. All. ampelinum-specific genes have putative functions related to polyamine metabolism and nickel assimilation. Congruently with the genome-based classification, All. vitis sensu stricto and All. ampelinum were clearly delineated by MALDI-TOF MS analysis. Moreover, our genome-based analysis indicated that Allorhizobium is clearly separated from other genera of the family Rhizobiaceae. ConclusionsComparative genomics and phylogenomic analysis provided novel insights into the diversification and taxonomy of Allorhizobium vitis species complex, supporting our redefinition of All. vitis sensu stricto and description of All. ampelinum. Our pan-genome analyses suggest that these species have differentiated ecologies, each relying on specialized nutrient consumption or toxic compound degradation to adapt to their respective niche.

genomics↗

bioRxiv2020

What drives the assembly of plant-associated protist microbiomes?

In a field experiment we investigated the influence of the environmental filters soil type and plant species identity on rhizosphere community assembly of Cercozoa, a dominant group of (mostly bacterivorous) soil protists. The experiment was set up with two plant species, lettuce and potato, grown in an experimental plot system with three contrasting soils. Plant species (14%) and rhizosphere origin (vs. bulk soil) with 13%, together explained four times more variation in cercozoan beta diversity than the three soil types (7% explained variation in beta diversity). Our results clearly confirm the existence of plant species-specific protist communities. Network analyses of bacteria-Cercozoa rhizosphere communities identified scale-free small world topologies, indicating mechanisms of self-organization. While the assembly of rhizosphere bacterial communities is bottom-up controlled through the resource supply from root (secondary) metabolites, our results support the hypothesis that the net effect may depend on the strength of top-down control by protist grazers. Since grazing of protists has a strong impact on the composition and functioning of bacteria communities, protists expand the repertoire of plant genes by functional traits, and should be considered as protist microbiomes in analogy to bacterial microbiomes. HighlightMicrobiomes of rhizosphere protists are plant species-specific and tightly co-evolving with their bacterial prey, thereby extending and modifying the functional repertoire of the bacterial-plant symbiosis.

plant biology↗

bioRxiv2019

PROMA PLASMIDS ARE INSTRUMENTAL IN THE DISSEMINATION OF LINURON CATABOLIC GENES BETWEEN DIFFERENT GENERA

PromA plasmids are broad host range plasmids, which are often cryptic and hence have an uncertain ecological role. We present three novel PromA {gamma} plasmids which carry genes associated with degradation of the phenylurea herbicide linuron, two (pPBL-H3-2 and pBPS33-2) of which originate from unrelated Hydrogenophaga hosts isolated from different environments, and one (pEN1) which was exogenously captured from an on-farm biopurification system. Both Hydrogenophaga plasmids carry all three necessary gene clusters determining the three main steps for conversion of linuron to Krebs cycle intermediates, while pEN1 only determines the initial linuron hydrolysis step. Linuron catabolic gene clusters that determine the same step were identical on all plasmids, encompassed in differently arranged constellations and characterized by the presence of multiple IS1071 elements. In all plasmids except pEN1, the insertion spot of the catabolic genes in the PromA {gamma} plasmids was the same. Highly similar PromA plasmids carrying the linuron degrading gene cargo at the same insertion spot were were previously identified in linuron degrading Variovorax sp. Interestingly, in both Hydrogenophaga populations not every PromA plasmid copy carries catabolic genes. The results indicate that PromA plasmids are important vehicles of linuron catabolic gene dissemination, rather than being cryptic and only important for the mobilization of other plasmids.

genomics↗

bioRxiv2018

The transferable resistome of produce

Produce is increasingly recognized as a reservoir of human pathogens and transferable antibiotic resistance genes. This study aimed to explore methods to characterize the transferable resistome of bacteria associated with produce. Mixed salad, arugula, and cilantro purchased from supermarkets were analyzed by means of cultivation- and DNA-based methods. Before and after a nonselective enrichment step, tetracycline (tet) resistant Escherichia coli were isolated and plasmids conferring tet resistance were captured by exogenous plasmid isolation. Tet resistant E. coli isolates, transconjugants and total community (TC)-DNA from the microbial fraction detached from leaves or after enrichment were analyzed for the presence of resistance genes, class 1 integrons and various plasmids by real-time PCR and PCR-Southern blot hybridization. Real-time PCR primers were developed for IncI and IncF plasmids. Tet resistant E. coli isolated from arugula and cilantro carried IncF, IncI1, IncN, IncH11, IncU and IncX1 plasmids. Three isolates from cilantro were positive for IncN plasmids and blaCTX-M-1. From mixed salad and cilantro, IncF, Inc11, and IncP-1{beta} plasmids were captured exogenously. Importantly, whereas direct detection of IncI and IncF plasmids in TC-DNA failed, these plasmids became detectable in DNA extracted from enrichment cultures. This confirms that cultivation-independent DNA-based methods are not always sufficiently sensitive to detect the transferable resistome in the rare microbiome. In summary, this study showed that an impressive diversity of self-transmissible multiple resistance plasmids was detected in bacteria associated with produce that is consumed raw, and exogenous capturing into E. coli suggests that they could transfer to gut bacteria as well.

microbiology↗