Effectiveness assessment of using riverine water eDNA to simultaneously monitor the riverine and riparian biodiversity information

Both aquatic and terrestrial biodiversity information can be detected in riverine water environmental DNA (eDNA). However, the effectiveness of using riverine water eDNA to simultaneously monitor the riverine and terrestrial biodiversity information remains unidentified. Here, we proposed that the monitoring effectiveness could be approximated by the transportation effectiveness of land-to-river and upstream-to-downstream biodiversity information flows and described by three new indicators. Subsequently, we conducted a case study in a watershed on the Qinghai–Tibet Plateau. The results demonstrated that there was higher monitoring effectiveness on summer or autumn rainy days than in other seasons and weather conditions. The monitoring of the bacterial biodiversity information was more efficient than the monitoring of the eukaryotic biodiversity information. On summer rainy days, 43–76% of species information in riparian sites could be detected in adjacent riverine water eDNA samples, 92–99% of species information in riverine sites could be detected in a 1-km downstream eDNA sample, and half of dead bioinformation (the bioinformation labeling the biological material that lacked life activity and fertility) could be monitored 4–6 km downstream for eukaryotes and 13–19 km downstream for bacteria. The current study provided reference method and data for future monitoring projects design and for future monitoring results evaluation.

Zero-Emission of Palm Oil Mill Effluent Final Discharge Promoted Bacterial Biodiversity Rebound in the Receiving Water System

Zero-emission technology for palm oil mill effluent (POME) has led to a breakthrough in the palm oil industry in relation to the goal of sustainable development. However, there are limited resources on how this technology has affected the bacterial community in the receiving river that has previously been polluted with POME final discharge. Thus, the current study assessed the recoverability of the unexplored bacterial community in the receiving water of a constructed river water system post-zero emission of POME final discharge. An artificial river water system was constructed in this study, where the viability status and the composition of the bacterial community were assessed for 15 days using a flow cytometry-based assay and high-throughput sequencing by Illumina MiSeq, respectively. The zero-emission of POME final discharge reduced not only the physicochemical properties and nutrient contents of the receiving water, but also the bacterial cells’ viability from 40.3% to 24.5% and shifted the high nucleic acid (HNA) to low nucleic acid (LNA) content (38.7% to 34.5%). The proposed POME bacterial indicators, Alcaligenaceae and Chromatiaceae were not detectable in the rainwater (control) but were detected in the artificial river water system after the introduction of POME final discharge at the compositions of 1.0–1.3% and 2.2–5.1%, respectively. The implementation of a zero-emission system decreased the composition of Chromatiaceae from 2.2% on day 8 until it was undetectable on day 15, while Alcaligenaceae was continuously reduced from 1.2% to 0.9% within that similar time frame. As indicated by principal coordinate (PCO) analysis, the reductions in biological oxygen demand (BOD5) would further diminish the compositions of these bioindicators. The zero-emission of POME final discharge has demonstrated its efficacy, not only in reducing the polluting properties, but also in the bacterial biodiversity rebound in the affected water system.

Mediterranean Spontaneously Fermented Sausages: Spotlight on Microbiological and Quality Features to Exploit Their Bacterial Biodiversity

The wide array of spontaneously fermented sausages of the Mediterranean area can represent a reservoir of microbial biodiversity and can be an important source of new technological and functional strains able to preserve product properties, counteracting the impoverishment of their organoleptic typical features due to the introduction of commercial starter cultures. We analysed 15 artisanal salamis from Italy, Spain, Croatia and Slovenia to evaluate the microbiota composition, through culture-dependent and culture-independent techniques (i.e., metagenomic analysis), chemical–physical features, biogenic amines and aroma profile. The final pH varied according to origin and procedures (e.g., higher pH in Italian samples due to long ripening and mold growth). Lactic acid bacteria (LAB) and coagulase-negative cocci (CNC) were the dominant population, with highest LAB counts in Croatian and Italian samples. Metagenomic analysis showed high variability in qualitative and quantitative microbial composition: among LAB, Latilactobacillus sakei was the dominant species, but Companilactobacillus spp. was present in high amounts (45–55% of the total ASVs) in some Spanish sausages. Among staphylococci, S. epidermidis, S. equorum, S. saprophyticus, S. succinus and S. xylosus were detected. As far as biogenic amines, tyramine was always present, while histamine was found only in two Spanish samples. These results can valorize the bacterial genetic heritage present in Mediterranean products, to find new candidates of autochthonous starter cultures or bioprotective agents.

Effectiveness Assessment of Using Riverine Water eDNA to Simultaneously Monitor the Riverine and Riparian Biodiversity Information

Both aquatic and terrestrial biodiversity information can be detected in riverine water environmental DNA (eDNA). However, the effectiveness of using riverine water eDNA to simultaneously monitor the riverine and terrestrial biodiversity information remains unidentified. Here, we proposed that the monitoring effectiveness could be approximated by the transportation effectiveness of land-to-river and upstream-to-downstream biodiversity information flows and described by three new indicators. Subsequently, we conducted a case study in a watershed on the Qinghai-Tibet Plateau. The results demonstrated that there was higher monitoring effectiveness on summer or autumn rainy days than in other seasons and weather conditions. The monitoring of the bacterial biodiversity information was more efficient than the monitoring of the eukaryotic biodiversity information. On summer rainy days, 43-76% of species information in riparian sites could be detected in water eDNA samples, 92-99% of species information in riverine sites could be detected in a 1-km downstream eDNA sample, and half of dead bioinformation (i.e., the bioinformation labeling the biological material that lacked life activity and fertility) could be monitored 4-6 km downstream for eukaryotes and 13-19 km downstream for bacteria. The current study provided reference method and data for future monitoring projects design and for future monitoring results evaluation.

Spatial variation of picoplankton communities along a cascade reservoir system in Patagonia, Argentina

In this study we explored how picoplankton community structure and diversity varied along three cascade oligo-mesotrophic reservoirs of the Limay River (Patagonia, Argentina): Alicura, Piedra del Águila and Ramos Mexía. We analyzed the spatial changes, covering lotic and lentic stretches along a gradient of 262 km from Andes to steppe, and we also sampled the main affluent of the Limay River (Collon Cura). In all sampling sites the main limnological variables were measured, and the picoplankton abundance (autotrophic and heterotrophic) was analyzed by flow cytometry. The bacterial biodiversity was assessed using high throughput sequencing Illumina MiSeq. We expected an increase in the trophic state along this series of cascade reservoirs, which would determine spatial differences in the structure of the picoplankton communities. We also hypothesized that the lotic and lentic conditions along the system would influence the bacterial composition. The results showed a slight increase in trophic state together with an increase in overall picoplankton abundance downstream, towards Ramos Mexía Reservoir. Picocyanobacteria were represented by phycoerythrin-rich cells all along the system, in accordance to the pattern described for oligotrophic aquatic ecosystems. Multivariate analyses based on bacterial OTU composition and environmental variables showed a spatial ordination of sites following the trend of increasing trophic state downstream. Molecular analyses of bacterial OTU diversity also showed an increase in richness and a decrease in evenness at the lotic stretches, and the opposite pattern in the reservoirs, suggesting that water retention time may play a role in structuring the community composition.

Does Organic Farming Increase Raspberry Quality, Aroma and Beneficial Bacterial Biodiversity?

Plant-associated microbes can shape plant phenotype, performance, and productivity. Cultivation methods can influence the plant microbiome structure and differences observed in the nutritional quality of differently grown fruits might be due to variations in the microbiome taxonomic and functional composition. Here, the influence of organic and integrated pest management (IPM) cultivation on quality, aroma and microbiome of raspberry (Rubus idaeus L.) fruits was evaluated. Differences in the fruit microbiome of organic and IPM raspberry were examined by next-generation sequencing and bacterial isolates characterization to highlight the potential contribution of the resident-microflora to fruit characteristics and aroma. The cultivation method strongly influenced fruit nutraceutical traits, aroma and epiphytic bacterial biocoenosis. Organic cultivation resulted in smaller fruits with a higher anthocyanidins content and lower titratable acidity content in comparison to IPM berries. Management practices also influenced the amounts of acids, ketones, aldehydes and monoterpenes, emitted by fruits. Our results suggest that the effects on fruit quality could be related to differences in the population of Gluconobacter, Sphingomonas, Rosenbergiella, Brevibacillus and Methylobacterium on fruit. Finally, changes in fruit aroma can be partly explained by volatile organic compounds (VOCs) emitted by key bacterial genera characterizing organic and IPM raspberry fruits.

The Effect of Biochar-Based Organic Amendments on the Structure of Soil Bacterial Community and Yield of Maize (Zea mays L.)

The taxonomic and functional diversity of bacteria in seven different experimental variants applied to soil under a maize plantation was determined by means of next-generation sequencing and biochemical methods. The aim of the study was to discover differences in the structure of bacteria and the level of soil enzymatic activity (BIF—biochemical index of fertility) after the application of a biofertiliser made of lignocellulosic substrate and biochar containing various microorganisms (algae, mycorrhizal fungi of the Glomus genus or the consortium of Bacillus sp. bacteria). The chemical composition and yield of crops was a measurable indicator of the effectiveness of the fertilisers. The biofertilisers influenced both the structure and the percentage share of individual bacterial operational taxonomic units (OTU). The cultivation of maize also modified qualitative and quantitative changes in the soil bacterial microbiome. A canonical variate analysis (CVA) showed that the soil pH exhibited a minimal positive correlation with the soil enzymatic activity and selected plant parameters, with the exception of the biofertiliser variant with arbuscular mycorrhiza (AM). Moreover, the AM biofertiliser significantly increased the BIF value, the yield of maize seeds and the starch content in the plants. The comprehensive nature of the research allowed for a deepening and systematization of the existing knowledge on the influence of biochar with the addition of selected microorganisms on the biochemical parameters of the soil and the bacterial biodiversity of the soil environment. Additionally, the inclusion of the chemical, sanitary composition and yield of maize in the research brought a measurable view of the changes taking place in the soil and plant environment under the influence of the discussed factor. Apart from the agronomic aspect (integrated crop cultivation—Directive 2009/128/EC) of our study, it was also closely related to environmental protection, as it proved that biochar-based biofertilisers could be an alternative to mineral fertilisation.

Diversity of Bacterioplankton and Bacteriobenthos from the Veracruz Reef System, Southwestern Gulf of Mexico

Bacterial diversity was explored among field samples and cultured isolates from coral reefs within the Veracruz Reef System. Bacterioplankton and bacteriobenthos were characterized by pyrosequencing 16S rRNA genes. Identified sequences belonged to the kingdom Bacteria and classified into 33 phyla. Proteobacteria (likely SAR11 clade) dominated in collective field samples, whereas Firmicutes were the most abundant taxa among cultured isolates. Bioinformatic sorting of sequences to family level revealed 223 bacterial families. Pseudomonadaceae, Exiguobacteraceae and Bacillaceae were dominant among cultured isolates. Vibrionaceae, Alteromonadaceae, and Flavobacteriaceae dominated in reef-associated sediments, whereas Rickettsiaceae and Synechoccaceae were more highly represented in the water column. Bacterial communities from sediments were more diverse than from the water column. This study reveals cryptic bacterial diversity among microenvironmental components of marine microbial reef communities subject to differential influence of anthropogenic stressors. Such investigations are critical for constructing scenarios of environmentally induced shifts in bacterial biodiversity and species composition.

The Less Expensive Choice: Bacterial Strategies to Achieve Successful and Sustainable Reciprocal Interactions

Bacteria, the first organisms that appeared on Earth, continue to play a central role in ensuring life on the planet, both as biogeochemical agents and as higher organisms’ symbionts. In the last decades, they have been employed both as bioremediation agents for cleaning polluted sites and as bioconversion effectors for obtaining a variety of products from wastes (including eco-friendly plastics and green energies). However, some recent reports suggest that bacterial biodiversity can be negatively affected by the present environmental crisis (global warming, soil desertification, and ocean acidification). This review analyzes the behaviors positively selected by evolution that render bacteria good models of sustainable practices (urgent in these times of climate change and scarcity of resources). Actually, bacteria display a tendency to optimize rather than maximize, to economize energy and building blocks (by using the same molecule for performing multiple functions), and to recycle and share metabolites, and these are winning strategies when dealing with sustainability. Furthermore, their ability to establish successful reciprocal relationships by means of anticipation, collective actions, and cooperation can also constitute an example highlighting how evolutionary selection favors behaviors that can be strategic to contain the present environmental crisis.

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

One of the most diverse ecological niches for microbial bioprospecting is soil, including that of drylands. Drylands are one of the most abundant biomes on Earth, but extreme cases, such as deserts, are considered very rare in Europe. The so-called Tabernas Desert is one of the few examples of a desert area in continental Europe, and although some microbial studies have been performed on this region, a comprehensive strategy to maximize the isolation of environmental bacteria has not been conducted to date. We report here a culturomics approach to study the bacterial diversity of this dryland by using a simple strategy consisting of combining different media, using serial dilutions of the nutrients, and using extended incubation times. With this strategy, we were able to set a large (254 strains) collection of bacteria, the majority of which (93%) were identified through 16S ribosomal RNA (rRNA) gene amplification and sequencing. A significant fraction of the collection consisted of Actinobacteria and Proteobacteria, as well as Firmicutes strains. Among the 254 isolates, 37 different genera were represented, and a high number of possible new taxa were identified (31%), of which, three new Kineococcus species. Moreover, 5 out of the 13 genera represented by one isolate were also possible new species. Specifically, the sequences of 80 isolates held a percentage of identity below the 98.7% threshold considered for potentially new species. These strains belonged to 20 genera. Our results reveal a clear link between medium dilution and isolation of new species, highlight the unexploited bacterial biodiversity of the Tabernas Desert, and evidence the potential of simple strategies to yield surprisingly large numbers of diverse, previously unreported, bacterial strains and species.