Plastisphere assemblages differ from the surrounding bacterial communities in transitional coastal environments.

Marine plastic contamination is currently considered ubiquitous in aquatic environments. These particles present a resistant and hydrophobic substrate known to promote microbial colonisation and biofilm formation in aquatic ecosystems, the so-called "Plastisphere", raising concerns about its potential ecological risks. The novelty of this topic translates into a relatively low number of studies, including for transitional coastal ecosystems, such as sandy beaches or estuarine habitats. Therefore, a sampling campaign was conducted in two transitional coastal ecosystems - the Mondego estuary (Portugal) - and adjacent sandy beaches (winter 2020). After visual sorting and filtering of suspected particles under sterile conditions DNA extraction and 16S rRNA amplicon high throughput sequencing was used to profile the bacterial communities on the surface of plastic particles and from those found on the water and sediments from the sampled transitional coastal ecosystems. All particles were characterised according to type, colour and size, and the chemical nature of the particles was determined by FTIR-ATR or µ-FTIR spectroscopy after DNA extraction. All samples contained plastics in several sizes (micro and mesoplastics), shapes (higher abundances of fragments on beaches and fibres in the estuarine waters), colours and polymers. Although no significant differences were detected in the α-diversity indexes of the bacterial communities between plastics and their surrounding environments, data showed the occurrence of unique key bacterial groups on plastics from both environments, such as pathogens (e.g., Lactococcus, Staphylococcus and Streptococcus) and groups commonly associated with wastewater treatment plants (e.g., members of the phylum Firmicutes). This highlights the concerns for plastics to act as vectors of transmission and spread of these bacterial groups in transitional coastal ecosystems. Furthermore, it raises the possibility that (micro)plastics entering the estuary from the sea play a substantial contribution to overall dynamics of (micro)plastics and their microbial assemblages in the estuarine system.

Identification and Characterization of Arbutus unedo L. Endophytic Bacteria Isolated from Wild and Cultivated Trees for the Biological Control of Phytophthora cinnamomi.

Arbutus unedo L. is a resilient tree with a circum-Mediterranean distribution. Besides its ecological relevance, it is vital for local economies as a fruit tree. Several microorganisms are responsible for strawberry tree diseases, leading to production constrictions. Thus, the development of alternative plant protection strategies is necessary, such as bacterial endophytes, which may increase their host's overall fitness and productivity. As agricultural practices are a driving factor of microbiota, this paper aimed to isolate, identify and characterize endophytic bacteria from strawberry tree leaves from plants growing spontaneously in a natural environment as well as from plants growing in orchards. A total of 62 endophytes were isolated from leaves and identified as Bacillus, Paenibacillus, Pseudomonas, Sphingomonas and Staphylococcus. Although a slightly higher number of species was found in wild plants, no differences in terms of diversity indexes were found. Sixteen isolates were tested in vitro for their antagonistic effect against A. unedo mycopathogens. B. cereus was the most effective antagonist causing a growth reduction of 20% in Glomerella cingulata and 40% in Phytophthora cinnamomi and Mycosphaerella aurantia. Several endophytic isolates also exhibited plant growth-promoting potential. This study provides insights into the diversity of endophytic bacteria in A. unedo leaves and their potential role as growth promoters and pathogen antagonists.

Effect of Low-Input Organic and Conventional Farming Systems on Maize Rhizosphere in Two Portuguese Open-Pollinated Varieties (OPV), "Pigarro" (Improved Landrace) and "SinPre" (a Composite Cross Population).

Maize is one of the most important crops worldwide and is the number one arable crop in Portugal. A transition from the conventional farming system to organic agriculture requires optimization of cultivars and management, the interaction of plant-soil rhizosphere microbiota being pivotal. The objectives of this study were to unravel the effect of population genotype and farming system on microbial communities in the rhizosphere of maize. Rhizosphere soil samples of two open-pollinated maize populations ("SinPre" and "Pigarro") cultivated under conventional and organic farming systems were taken during flowering and analyzed by next-generation sequencing (NGS). Phenological data were collected from the replicated field trial. A total of 266 fungi and 317 bacteria genera were identified in "SinPre" and "Pigarro" populations, of which 186 (69.9%) and 277 (87.4%) were shared among them. The microbiota of "Pigarro" showed a significant higher (P < 0.05) average abundance than the microbiota of "SinPre." The farming system had a statistically significant impact (P < 0.05) on the soil rhizosphere microbiota, and several fungal and bacterial taxa were found to be farming system-specific. The rhizosphere microbiota diversity in the organic farming system was higher than that in the conventional system for both varieties. The presence of arbuscular mycorrhizae (Glomeromycota) was mainly detected in the microbiota of the "SinPre" population under the organic farming systems and very rare under conventional systems. A detailed metagenome function prediction was performed. At the fungal level, pathotroph-saprotroph and pathotroph-symbiotroph lifestyles were modified by the farming system. For bacterial microbiota, the main functions altered by the farming system were membrane transport, transcription, translation, cell motility, and signal transduction. This study allowed identifying groups of microorganisms known for their role as plant growth-promoting rhizobacteria (PGPR) and with the capacity to improve crop tolerance for stress conditions, allowing to minimize the use of synthetic fertilizers and pesticides. Arbuscular mycorrhizae (phyla Glomeromycota) were among the most important functional groups in the fungal microbiota and Achromobacter, Burkholderia, Erwinia, Lysinibacillus, Paenibacillus, Pseudomonas, and Stenotrophomonas in the bacterial microbiota. In this perspective, the potential role of these microorganisms will be explored in future research.

Draft Genome Resources Sequences of Six Pseudomonas syringae pv. actinidiae Strains Isolated from Actinidia chinensis var. deliciosa Leaves in Portugal.

Pseudomonas syringae pv. actinidiae is a quarantine bacterium affecting all the Portuguese main areas of kiwifruit production. We report the draft genome of six P. syringae pv. actinidiae strains isolated from symptomatic leaves of Actinidia chinensis var. deliciosa in a study that determined the genetic population structure of the endophytic and epiphytic populations in two consecutive seasons. Average nucleotide identity values were above 99% similarity with reference strains from P. syringae pv. actinidiae biovar 3. The genomic differences found between these strains confirm the genetic diversity described for P. syringae pv. actinidiae population in Portugal. Furthermore, data provide evidence that the initial clonal expansion of P. syringae pv. actinidiae in Europe was followed by a genomic diversification constituting a valuable resource for epidemiological and evolutionary studies, namely when adopting strategies for epidemics management.

Genetic Diversity of Pseudomonas syringae pv. actinidiae: Seasonal and Spatial Population Dynamics.

Pseudomonassyringae pv. actinidiae (Psa) is a gram-negative bacterium responsible for the bacterial canker in Actinidia chinensis var. deliciosa and A. chinensis var. chinensis, a quarantine organism threatening the kiwifruit industry sustainability. The present study aimed to determine the genetic structure of the endophytic and epiphytic populations of Psa isolated from four different Portuguese orchards with distinct abiotic conditions in two consecutive seasons. The results identified several coexisting and highly heterogeneous Psa populations. Moreover, evident changes in population structure occurred between the epiphytic and endophytic populations, and between seasons with a notable decrease in Psa diversity in autumn. This work provided solid evidence that the initial clonal expansion of Psa in Europe was followed by a wide genomic diversification. This perspective is important for the understanding of kiwifruit bacterial canker disease occurrence and Psa evolution, namely when adopting strategies for management of epidemics.