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.

Matching times: Trying to improve the correlation between heavy metal levels in mosses and bulk deposition

The relationship between the concentrations of metals in moss tissues and atmospheric deposition is highly complex, resulting in a general lack of correlations between these two matrices. Here, we tried to improve the significance of the moss-bulk deposition (BD) relationship by eliminating the mismatch between the time that the moss tissue selected for analysis is exposed to atmospheric deposition, and the time during which BD is collected. For this, we analysed the concentrations of Cd, Hg and Pb in new grown tissue of Pseudoscleropodium purum and BD collected monthly, for one year, in 21 sampling sites (SS) under different degrees of pollution. Additionally, we assessed how different moss tissues, including native moss (green parts and new grown tissues of P. purum) and moss transplants of Sphagnum denticulatum, reflect BD to find out which moss tissues provide a better estimate of the atmospheric deposition of heavy metals. First of all, our results showed that eliminating the mismatch between native moss exposure time and BD collection period is not enough to improve their correlation. Environmental variation emerged as the main driver of tissue content variation altering the moss-BD relationship unpredictably. Secondly, native P. purum represents BD values better than devitalized transplants by displaying a greater number of significant correlations with BD. Specifically, green parts of P. purum generally represent better BD than new grown tissues. Overall, we conclude that neither native mosses nor transplants are good estimators of atmospheric heavy metal deposition rates. However, they are good qualitative indicators of the atmospheric deposition, by allowing us to differentiate SS subject to a wide range of pollution levels. Additionally, green parts of P. purum, and likely of other mosses with similar growth forms, should be used in passive biomonitoring studies to make results from different studies comparable.

Characterization of Pseudomonas syringae pv. actinidiae biovar 3 on kiwifruit in north-west Portugal

AIMS

Bacterial kiwifruit canker disease, caused by Pseudomonas syringae pv. actinidiae (Psa) was detected in north-west Portugal in 2010, and has since caused significant losses. The objectives of this work were to characterize the Portuguese population(s) of Psa and to define the actual prevalence of Psa biovars in the most productive kiwifruit region in Portugal.

METHODS AND RESULTS

Isolates obtained from Actinidia deliciosa orchards were characterized by morphological, biochemical, physiological, fatty acids and molecular tests (PCR, BOX-PCR, duplex-PCR, multiplex-PCR and RFLP), phaseolotoxin, housekeeping and effector genes and pathogenicity. Results established that only Psa biovar 3 is present in the north-west of Portugal, despite phenotypic and genetic variability among the isolates.

CONCLUSIONS

This work provides new information on P. syringae pv. actinidiae (Psa) genetic profile in Portugal, indicating for the first time, that two genetically different subpopulations of Psa biovar 3 are present.

SIGNIFICANCE AND IMPACT OF THE STUDY

A new subpopulation of Psa biovar 3 was found for the first time in Portugal, contributing to increase knowledge about this population worldwide and to support further understanding of the impact of Psa.

Detection and characterization of Pseudomonas syringae pv. actinidifoliorum in kiwifruit in Spain

AIMS

Bacterial canker of kiwifruit caused by Pseudomonas syringae pv. actinidiae (Psa) is currently the major threat to its commercial production worldwide. In 2011, the most virulent type (Psa3) was detected for the first time in Northwest-Spain, in the province of Pontevedra. In 2013 surveys, leaves and flower buds with mild symptoms were observed in Actinidia deliciosa 'Hayward' vines in an orchard at the province of A Coruña, suggesting the presence of P. syringae pv. actinidifoliorum (Psaf).

METHODS AND RESULTS

Isolates obtained from such orchard were characterized by morphological, biochemical and physiological tests, fatty acids (FA) profile and molecular tests (PCR, BOX-PCR, duplex PCR, multiplex PCR, real-time PCR, PCR-C, phytotoxins, housekeeping and effector genes). Pathogenicity tests were also carried out on plants and fruits of A. deliciosa 'Hayward' and on different cultivated plants and fruits. Results demonstrated the presence of P. syringae pv. actinidifoliorum in Spain.

CONCLUSIONS

The work provides new information on the pathovar P. syringae pv. actinidifoliorum, which has only been found previously in New Zealand, Australia and France.

SIGNIFICANCE AND IMPACT OF STUDY

The results are relevant for taxonomy of isolates of P. syringae from kiwifruit, especially those of low virulence not belonging to pathovar actinidiae.

Active biomonitoring with the moss Pseudoscleropodium purum: Comparison between different types of transplants and bulk deposition

Active biomonitoring with terrestrial mosses can be used to complement traditional air pollution monitoring techniques. Several studies have been carried out to compare the uptake capacity of different types of moss transplants. However, until now the relationship between the uptake of elements in devitalized moss bags and in irrigated transplants has not been explored. In this study, the final concentrations of Cd, Cu, Hg, Pb and Zn were determined in irrigated and devitalized moss transplants in the surroundings of a steelworks. The concentrations were also compared with those of the same elements in the bulk deposition to determine which type of moss transplant yields the closest correlations. Devitalized moss retained higher concentrations of all of the elements (except Hg) than the irrigated moss. Both irrigated and devitalized moss transplants appear to detect the same type of contamination (i.e. particulate matter and dissolved metals rather than gaseous forms) as significant correlations were found for Cu, Hg, Pb and Zn, whereas, neither type of the moss transplant was sensitive enough to detect changes in the soluble fraction load of bulk deposition. Further studies will be needed to a better understanding of the correlation between the concentrations of elements in moss transplants with the particulate fraction of the bulk deposition. This will enable the establishment of a more robust and accurate biomonitoring tool.

Distinguishing metal bioconcentration from particulate matter in moss tissue: testing methods of removing particles attached to the moss surface

Accurate differentiation of the proportion of bioconcentrated metals (i.e. incorporated into cells) and the proportion that is not bioconcentrated (i.e. adsorbed at the surface) would lead to a better understanding of the uptake processes and would represent an advance in the use of mosses as biomonitors. Traditionally the methods used to remove contaminants that are not bioconcentrated were to wash the plant material with water or to apply the sequential elution technique, but nowadays both options are considered inaccurate for these purposes. The remaining possibilities are to clean the moss samples with a nitrogen jet or by power ultrasound. Samples of terrestrial moss Pseudoscleropodium purum (Hewd.) Fleisch. were collected from five sampling stations. Different nitrogen jet cleaning procedures and ultrasound cleaning procedures were applied to the mosses. To determine whether any of the treatments altered the membrane integrity of the moss samples, the concentrations of K were determined. The shoots were observed under a scanning electron microscope, and the size and number of particles were determined. Nitrogen jet cleaning was determined to be unacceptable because it damaged the phyllids and/or altered the membrane permeability and did not eliminate the particles from the moss surface. Moreover, ultrasound cleaning treatment should also discarded because of the loss of extracellular metals that are transferred to the water in which the moss is cleaned.

Moss bag biomonitoring: a methodological review

Although the moss bag technique has been used for active biomonitoring for the past 40years, there is still no standardized protocol that enables application of the technique as a tool to monitor air quality. The aim of this review paper is to evaluate the degree of standardization of each of the variables that must be considered in applying the technique (i.e. the variables associated with preparation of the moss and moss bags, exposure of the bags, and post-exposure treatment). For this purpose, 112 scientific papers that report the methods used in applying the moss bag technique were consulted. Finally, on the basis of the conclusions reached, we propose a protocol that will enable each of these variables to be investigated separately, with the final aim of developing a standardized methodology.

Photosynthesis, carbohydrate storage and survival of a native and an introduced tree species in relation to light and defoliation

Fraxinus uhdei (Wenz.) Lingelsh (tropical ash), a species introduced to Hawaii from Mexico, invades forests of the endemic tree Acacia koa A.Gray (koa). We examined physiological and morphological characteristics of koa and tropical ash to explore possible mechanisms that may facilitate invasion of koa forests by tropical ash. Seedlings of both species were grown in a greenhouse in three light treatments: 100% photosynthetic photon flux (PPF); 18% PPF; and 2% PPF inside the greenhouse. Light compensation point, maximum CO2 assimilation rate and dark respiration rate of seedlings differed significantly among light treatments, but were similar between species. A defoliation experiment indicated that tropical ash was better able to survive defoliation than koa, especially under high-light conditions. Tropical ash seedlings allocated more carbon (C) and nitrogen (N) to storage per unit PPF than koa seedlings. Total nonstructural carbohydrates were positively correlated with plant survival in both species. The patterns of C and N allocation associated with tropical ash seedlings favor their survival in high light, under intense herbivory and on sites where N availability is seasonal or highly variable. Variation in carbohydrate storage between koa and tropical ash greatly exceeded variation in photosynthetic performance at the leaf level.

Water supply regulates structure, productivity, and water use efficiency of Acacia koa forest in Hawaii

We studied changes in stand structure, productivity, canopy development, growth efficiency, and intrinsic water use efficiency (WUE=photosynthesis/stomatal conductance) of the native tree koa (Acacia koa) across a gradient of decreasing rainfall (2600-700 mm) with increasing elevation (700-2000 m) on the island of Hawaii. The stands were located on organic soils on either smooth (pahoehoe) or rough (aa) lava flows. In the greenhouse, we also examined growth and WUE responses to different water regimes of koa seedlings grown from seeds collected in the study area. We tested the hypotheses that (1) stand basal area, aboveground net primary productivity (ANPP), leaf area index (LAI), and growth per unit leaf area decreased with decreasing rainfall, (2) WUE increased with decreasing rainfall or water supply, and (3) WUE responses were caused by stomatal limitation rather than by nutrient limitations to photosynthesis. The carbon isotope composition of phyllode tissues (δ¹³C) was examined as an integrated measure of WUE. Basal area and LAI of koa stands on both pahoehoe and aa lava flows, and ANPP on aa lava flows decreased with elevation. Basal area, LAI, and ANPP of koa in mixed stands with the exotic tropical ash (Fraxinus udhei) were lower compared to single-species koa stands at similar elevations. Along the gradient, phyllode δ¹³C (and therefore WUE) increased with elevation from -30.2 to -26.8‰. Koa in mixed stands exhibited higher (less negative) δ¹³C than in single-species stands suggesting that koa and tropical ash competed for water. In the greenhouse, we observed the same trend observed in the field, as phyllode δ¹³C increased from -27.7 to -24‰ as water supply decreased. Instantaneous gas exchange measurements in the greenhouse showed an inverse correlation of both maximum (morning) photosynthesis (A) and conductance (g) with δ¹³C values and, also, a good agreement between instantaneous (A/g) and integrated measures of WUE. Phyllode δ¹³C was not correlated with foliar concentrations of N or other nutrients in either the field or the greenhouse, indicating that differences in δ¹³C were caused by stomatal limitation rather than by nutrient-related changes in photosynthetic capacity. This study provided evidence that long-term structural and growth adjustments as well as changes in WUE are important mechanisms of koa response to water limitation.

Growth, biomass allocation and photosynthesis of invasive and native Hawaiian rainforest species

Growth, biomass allocation, and photosynthetic characteristics of seedlings of five invasive non-indigenous and four native species grown under different light regimes were studied to help explain the success of invasive species in Hawaiian rainforests. Plants were grown under three greenhouse light levels representative of those found in the center and edge of gaps and in the understory of Hawaiian rainforests, and under an additional treatment with unaltered shade. Relative growth rates (RGRs) of invasive species grown in sun and partial shade were significantly higher than those for native species, averaging 0.25 and 0.17 g g^-1 week^-1, respectively, while native species averaged only 0.09 and 0.06 g g^-1 week^-1, respectively. The RGR of invasive species under the shade treatment was 40% higher than that of native species. Leaf area ratios (LARs) of sun and partial-shade-grown invasive and native species were similar but the LAR of invasive species in the shade was, on average, 20% higher than that of native species. There were no differences between invasive and native species in biomass allocation to shoots and roots, or in leaf mass per area across light environments. Light-saturated photosynthetic rates (Pmax) were higher for invasive species than for native species in all light treatments. Pmax of invasive species grown in the sun treatment, for example, ranged from 5.5 to 11.9 μmol m^-2 s^-1 as compared with 3.0-4.5 μmol m^-2 s^-1 for native species grown under similar light conditions. The slope of the linear relationship between Pmax and dark respiration was steeper for invasive than for native species, indicating that invasive species assimilate more CO₂ at a lower respiratory cost than native species. These results suggest that the invasive species may have higher growth rates than the native species as a consequence of higher photosynthetic capacities under sun and partial shade, lower dark respiration under all light treatments, and higher LARs when growing under shade conditions. Overall, invasive species appear to be better suited than native species to capturing and utilizing light resources, particularly in high-light environments such as those characterized by relatively high levels of disturbance.