Biomonitoring for the 21st Century: Integrating Next-Generation Sequencing Into Ecological Network Analysis

Revisiting the current and emerging concepts of postharvest fresh fruit and vegetable pathology for next-generation antifungal technologies

Fungal infections of fresh fruits and vegetables (FFVs) can lead to safety problems, including consumer poisoning by mycotoxins. Various strategies exist to control fungal infections of FFVs, but their effectiveness and sustainability are limited. Recently, new concepts based on the microbiome and pathobiome have emerged and offer a more holistic perspective for advancing postharvest pathogen control techniques. Understanding the role of the microbiome in FFV infections is essential for developing sustainable control strategies. This review examines current and emerging approaches to postharvest pathology. It reviews what is known about the initiation and development of infections in FFVs. As a promising concept, the pathobiome offers new insights into the basic mechanisms of microbial infections in FFVs. The underlying mechanisms uncovered by the pathobiome are being used to develop more relevant global antifungal strategies. This review will also focus on new technologies developed to target the microbiome and members of the pathobiome to control infections in FFVs and improve safety by limiting mycotoxin contamination. Specifically, this review stresses emerging technologies related to FFVs that are relevant for modifying the interaction between FFVs and the microbiome and include the use of microbial consortia, the use of genomic technology to manipulate host and microbial community genes, and the use of databases, deep learning, and artificial intelligence to identify pathobiome markers. Other approaches include programming the behavior of FFVs using synthetic biology, modifying the microbiome using sRNA technology, phages, quorum sensing, and quorum quenching strategies. Rapid adoption and commercialization of these technologies are recommended to further improve the overall safety of FFVs.

Mitigating the impacts of street lighting on biodiversity and ecosystem functioning

Street lights are not only a major source of direct light pollution emissions, but stock has been transitioning to light-emitting diode (LED) technology in many parts of the world, resulting in increases in the blue part of the visible spectrum that is more harmful to biodiversity and human health. But LEDs can be modified more easily than conventional sodium lamps by adjusting their intensity, spectral output and other features of street light systems. In this Opinion piece, I provide an updated overview of street light mitigation strategies and contend that research in this area has been slow. I show how experimental lighting rigs that mimic real street lights can be used for mitigation testing, since invertebrate behaviour, abundances and interactions can respond quickly and measurably. I demonstrate how advances in network ecology that use species interaction data can provide much-needed assessments of the impacts of street lights on biodiversity and ecosystem functioning, and ultimately provide new tools and metrics for biomonitoring. I acknowledge the limitations of measuring local, short-term responses of biodiversity and identify promising avenues for collaborating with industry and government agencies in new or existing road lighting schemes, to minimize the negative long-term impacts at marginal cost. This article is part of the theme issue 'Light pollution in complex ecological systems'.

Bacteriophage-based biosensors for detection of pathogenic microbes in wastewater

Wastewater is discarded from several sources, including industry, livestock, fertilizer application, and municipal waste. If the disposed of wastewater has not been treated and processed before discharge to the environment, pathogenic microorganisms and toxic chemicals are accumulated in the disposal area and transported into the surface waters. The presence of harmful microbes is responsible for thousands of human deaths related to water-born contamination every year. To be able to take the necessary step and quick action against the possible presence of harmful microorganisms and substances, there is a need to improve the effective speed of identification and treatment of these problems. Biosensors are such devices that can give quantitative information within a short period of time. There have been several biosensors developed to measure certain parameters and microorganisms. The discovered biosensors can be utilized for the detection of axenic and mixed microbial strains from the wastewaters. Biosensors can further be developed for specific conditions and environments with an in-depth understanding of microbial organization and interaction within that community. In this regard, bacteriophage-based biosensors have become a possibility to identify specific live bacteria in an infected environment. This paper has investigated the current scenario of microbial community analysis and biosensor development in identifying the presence of pathogenic microorganisms.

Ecological linkages between biotechnologically relevant autochthonous microorganisms and phenolic compounds in sugar apple fruit (Annona squamosa L.)

Our study investigated the potential of Annona squamosa (L.) fruit as a reservoir of yeasts and lactic acid bacteria having biotechnological implications, and phenolics capable of modifying the ecology of microbial consortia. Only a single species of lactic acid bacteria (Enterococcus faecalis) was identified, while Annona fruit seemed to be a preferred niche for yeasts (Saccharomyces cerevisiae, Hanseniaspora uvarum), which were differentially distributed in the fruit. In order to identify ecological implications for inherent phenolics, the antimicrobial potential of water- and methanol/water-soluble extracts from peel and pulp was studied. Pulp extracts did not show any antimicrobial activity against the microbial indicators, while some Gram-positive bacteria (Staphylococcus aureus, Staphylococcus saprophyticus, Listeria monocytogenes, Bacillus megaterium) were susceptible to peel extracts. Among lactic acid bacteria used as indicators, only Lactococcus lactis and Weissella cibaria were inhibited. The chemical profiling of methanol/water-soluble phenolics from Annona peel reported a full panel of 41 phenolics, mainly procyanidins and catechin derivatives. The antimicrobial activity was associated to specific compounds (procyanidin dimer type B [isomer 1], rutin [isomer 2], catechin diglucopyranoside), in addition to unidentified catechin derivatives. E. faecalis, which was detected in the epiphytic microbiota, was well adapted to the phenolics from the peel. Peel phenolics had a growth-promoting effect toward the autochthonous yeasts S. cerevisiae and H. uvarum.

The predator problem and PCR primers in molecular dietary analysis: swamped or silenced; depth or breadth?

Dietary metabarcoding has vastly improved our ability to analyse the diets of animals, but it is hampered by a plethora of technical limitations including potentially reduced data output due to the disproportionate amplification of the DNA of the focal predator, here termed 'the predator problem'. We review the various methods commonly used to overcome this problem, from deeper sequencing to exclusion of predator DNA during PCR, and how they may interfere with increasingly common multi-predator-taxon studies. We suggest that multi-primer approaches with an emphasis on achieving both depth and breadth of prey detections may overcome the issue to some extent, although multi-taxon studies require further consideration, as highlighted by an empirical example. We also review several alternative methods for reducing the prevalence of predator DNA that are conceptually promising but require additional empirical examination. The predator problem is a key constraint on molecular dietary analyses but, through this synthesis, we hope to guide researchers in overcoming this in an effective and pragmatic way.

A network simplification approach to ease topological studies about the food-web architecture

Food webs studies are intrinsically complex and time-consuming. Network data about trophic interaction across different large locations and ecosystems are scarce in comparison with general ecological data, especially if we consider terrestrial habitats. Here we present a complex network strategy to ease the gathering of the information by simplifying the collection of data with a taxonomic key. We test how well the topology of three different food webs retain their structure at the resolution of the nodes across distinct levels of simplification, and we estimate how community detection could be impacted by this strategy. The first level of simplification retains most of the general topological indices; betweenness and trophic levels seem to be consistent and robust even at the higher levels of simplification. This result suggests that generalisation and standardisation, as a good practice in food webs science, could benefit the community, both increasing the amount of open data available and the comparison among them, thus providing support especially for scientists that are new in this field and for exploratory analysis.

Comparison of materials for rapid passive collection of environmental DNA

Passive collection is an emerging sampling method for environmental DNA (eDNA) in aquatic systems. Passive eDNA collection is inexpensive and efficient, and requires minimal equipment, making it suited to high‐density sampling and remote deployment. Here, we compare the effectiveness of nine membrane materials for passively collecting fish eDNA from a 3‐million‐litre marine mesocosm. We submerged materials (cellulose, cellulose with 1% and 3% chitosan, cellulose overlayed with electrospun nanofibres and 1% chitosan, cotton fibres, hemp fibres, and sponge with either zeolite or active carbon) for intervals between 5 and 1080 min. We show that for most materials, with as little as 5 min of submersion, mitochondrial fish eDNA measured with qPCR, and fish species richness measured with metabarcoding, was comparable to that collected by conventional filtering. Furthermore, PCR template DNA concentrations and species richness were generally not improved significantly by longer submersion. Species richness detected for all materials ranged between 11 and 37 species, with a median of 27, which was comparable to the range for filtered eDNA (19–32). Using scanning electron microscopy, we visualized biological matter adhering to the surface of materials, rather than entrapped, with images also revealing a diversity in size and structure of putative eDNA particles. eDNA can be collected rapidly from seawater with a passive approach and using a variety of materials. This will suit cost‐ and time‐sensitive biological surveys, and where access to equipment is limited.

Renaissance for Phage-Based Bacterial Control

Bacteriophages (phages) are an underutilized biological resource with vast potential for pathogen control and microbiome editing. Phage research and commercialization have increased rapidly in biomedical and agricultural industries, but adoption has been limited elsewhere. Nevertheless, converging advances in DNA sequencing, bioinformatics, microbial ecology, and synthetic biology are now poised to broaden phage applications beyond pathogen control toward the manipulation of microbial communities for defined functional improvements. Enhancements in sequencing combined with network analysis make it now feasible to identify and disrupt microbial associations to elicit desirable shifts in community structure or function, indirectly modulate species abundance, and target hub or keystone species to achieve broad functional shifts. Sequencing and bioinformatic advancements are also facilitating the use of temperate phages for safe gene delivery applications. Finally, integration of synthetic biology stands to create novel phage chassis and modular genetic components. While some fundamental, regulatory, and commercialization barriers to widespread phage use remain, many major challenges that have impeded the field now have workable solutions. Thus, a new dawn for phage-based (chemical-free) precise biocontrol and microbiome editing is on the horizon to enhance, suppress, or modulate microbial activities important for public health, food security, and more sustainable energy production and water reuse.

Bacterial community demonstrates stronger network connectivity than fungal community in desert-grassland salt marsh

The diversity of soil bacterial and fungal communities is closely related to the soil characteristics and vegetation types in salt marsh ecosystems, but the biogeographic patterns and driving factors in desert-grassland salt marsh (DGSM) are still unclear. In this study, we divided sample plots according to the dominant species in Jiantan Lake wetland of a typical DGSM in Northwestern China. The effects of different environmental factors and halophytes on the structure of soil bacterial and fungal communities were investigated using soil physicochemical characterization and high-throughput sequencing analysis. The diversity of bacterial communities in bulk soil and three dominant halophytes (Kalidium cuspidatum, Nitraria tangutorum and Sophora alopecuroides) were the main factors affecting soil physicochemical properties and halophyte vegetation coverage. Proteobacteria, Bacteroides and Gemmatimonadetes had the highest abundance in bulk soil and the lowest in Sophora alopecuroides sample soil; the opposite was true for Acidobacteria and Chloroflexi. The abundance of Ascomycota in bulk soil and Sophora alopecuroides sample soil was higher than Kalidium cuspidatum and Nitraria tangutorum sample soils, whereas the Mortierellomycota was the highest in Nitraria tangutorum sample soil. Co-occurrence network analysis showed that halophyte cover increased the connectivity and complexity of the bacterial-fungal interaction network, and the halophytic shrub sample soil had a more stable network relationship than the halophytic herb soil. The key taxa of each plot were identified through network relationships. It was found that the keystone taxa of Proteobacteria, Firmicutes, Ascomycota and Chytridiomycota played important roles in maintaining community functions, and most of them were not significantly influenced by soil physicochemical properties. The results of this study provide new insights for a deeper understanding of the halophytes that drive the multifunctionality and stability of soil ecosystems in DGSM.

Nitrogen cycling processes and the role of multi-trophic microbiota in dam-induced river-reservoir systems

The nitrogen (N) cycle is one of the most important nutrient cycles in river systems, and it plays an important role in maintaining biogeochemical balance and global climate stability. One of the main ways that humans have altered riverine ecosystems is through the construction of hydropower dams, which have major effects on biogeochemical cycles. Most previous studies examining the effects of damming on N cycling have focused on the whole budget or flux along rivers, and the role of river as N sources or sinks at the global or catchment scale. However, so far there is still lack of comprehensive and systematic summarize on N cycling and the controlling mechanisms in reservoirs affected by dam impoundment. In this review, we firstly summarize N cycling processes along the longitudinal riverine-transition-lacustrine gradient and the vertically stratified epilimnion-thermocline-hypolimnion gradient. Specifically, we highlight the direct and indirect roles of multi-trophic microbiota and their interactions in N cycling and discuss the main factors controlling these biotic processes. In addition, future research directions and challenges in incorporating multi-trophic levels in bioassessment, environmental flow design, as well as reservoir regulation and restoration are summarized. This review will aid future studies of N fluxes along dammed rivers and provide an essential reference for reservoir management to meet ecological needs.

Measurements of the swimming speeds of motile microorganisms using object tracking and their correlation with water pollution and rheology levels

Self-propelled microscopic organisms are ubiquitous in water. Such organisms' motility depends on hydrodynamic and physical factors related to the rheology of the surrounding media and biological factors depending on the organisms' state and well-being. Here we demonstrate that the swimming speed of Paramecium aurelia, a unicellular protozoan, globally found in fresh, brackish, and salt waters, can be used as a measurable frugal indicator of the presence of pollutants in water. This study establishes a significant and consistent relationship between Paramecia's swimming speed and the presence of five different organic and inorganic contaminants at varying concentrations centered around drinking water thresholds. The large size and ubiquity of the targeted microorganism, the avoidance of reagents or specialized tools for the measurement, and the simple data collection based on an object tracking algorithm enable the automatization of the assessment and real-time results using globally available technology.

Responses of juvenile fathead minnow (Pimephales promelas) gut microbiome to a chronic dietary exposure of benzo[a]pyrene

The microbiome has been described as an additional host "organ" with well-established beneficial roles. However, the effects of exposures to chemicals on both structure and function of the gut microbiome of fishes are understudied. To determine effects of benzo[a]pyrene (BaP), a model persistent organic pollutant, on structural shifts of gut microbiome in juvenile fathead minnows (Pimephales promelas), fish were exposed ad libitum in the diet to concentrations of 1, 10, 100, or 1000 μg BaP g^-1 food, in addition to a vehicle control, for two weeks. To determine the link between exposure to BaP and changes in the microbial community, concentrations of metabolites of BaP were measured in fish bile and 16S rRNA amplicon sequencing was used to evaluate the microbiome. Exposure to BaP only reduced alpha-diversity at the greatest exposure concentrations. However, it did alter community composition assessed as differential abundance of taxa and reduced network complexity of the microbial community in all exposure groups. Results presented here illustrate that environmentally-relevant concentrations of BaP can alter the diversity of the gut microbiome and community network connectivity.

A dearth of data: fitting parasitoids into ecological networks

Studying parasitoids can provide insights into global diversity estimates, climate change impacts, and agroecosystem service provision. However, this potential remains largely untapped due to a lack of data on how parasitoids interact with other organisms. Ecological networks are a useful tool for studying and exploiting the impacts of parasitoids, but their construction is hindered by the magnitude of undescribed parasitoid species, a sparse knowledge of host ranges, and an under-representation of parasitoids within DNA-barcode databases (we estimate <5% have a barcode). Here, we advocate the use of DNA metabarcoding to construct the host-parasitoid component of multilayer networks. While the incorporation of parasitoids into network-based analyses has far ranging applications, we focus on its potential for assessing ecosystem service provision within agroecosystems.

Passive eDNA collection enhances aquatic biodiversity analysis

Environmental DNA (eDNA) metabarcoding is a sensitive and widely used approach for species detection and biodiversity assessment. The most common eDNA collection method in aquatic systems is actively filtering water through a membrane, which is time consuming and requires specialized equipment. Ecological studies investigating species abundance or distribution often require more samples than can be practically collected with current filtration methods. Here we demonstrate how eDNA can be passively collected in both tropical and temperate marine systems by directly submerging filter membranes (positively charged nylon and non-charged cellulose ester) in the water column. Using a universal fish metabarcoding assay, we show that passive eDNA collection can detect fish as effectively as active eDNA filtration methods in temperate systems and can also provide similar estimates of total fish biodiversity. Furthermore, passive eDNA collection enables greater levels of biological sampling, which increases the range of ecological questions that eDNA metabarcoding can address.

Bessey et al. present a method of passive eDNA collection from marine aquatic systems. This approach enables lower cost, high throughput sampling of aquatic environments and demonstrably collects high levels of eDNA for biodiversity studies.

Microbial networks inferred from environmental DNA data for biomonitoring ecosystem change: Strengths and pitfalls

Environmental DNA contains information on the species interaction networks that support ecosystem functions and services. Next-generation biomonitoring proposes the use of this data to reconstruct ecological networks in real time and then compute network-level properties to assess ecosystem change. We investigated the relevance of this proposal by assessing: (i) the replicability of DNA-based networks in the absence of ecosystem change, and (ii) the benefits and shortcomings of community- and network-level properties for monitoring change. We selected crop-associated microbial networks as a case study because they support disease regulation services in agroecosystems and analysed their response to change in agricultural practice between organic and conventional systems. Using two statistical methods of network inference, we showed that network-level properties, especially β-properties, could detect change. Moreover, consensus networks revealed robust signals of interactions between the most abundant species, which differed between agricultural systems. These findings complemented those obtained with community-level data that showed, in particular, a greater microbial diversity in the organic system. The limitations of network-level data included (i) the very high variability of network replicates within each system; (ii) the low number of network replicates per system, due to the large number of samples needed to build each network; and (iii) the difficulty in interpreting links of inferred networks. Tools and frameworks developed over the last decade to infer and compare microbial networks are therefore relevant to biomonitoring, provided that the DNA metabarcoding data sets are large enough to build many network replicates and progress is made to increase network replicability and interpretation.

The Nexus Between Plant and Plant Microbiome: Revelation of the Networking Strategies

The diversity of plant-associated microbes is enormous and complex. These microbiomes are structured and form complex interconnected microbial networks that are important in plant health and ecosystem functioning. Understanding the composition of the microbiome and their core function is important in unraveling their networking strategies and their potential influence on plant performance. The network is altered by the host plant species, which in turn influence the microbial interaction dynamics and co-evolution. We discuss the plant microbiome and the complex interplay among microbes and between their host plants. We provide an overview of how plant performance is influenced by the microbiome diversity and function.

Use of ecosystem health indicators for assessing anthropogenic impacts on freshwaters in Argentina: a review

Indicators of ecosystem health are effective tools to assess freshwater ecosystem impairment. However, they are scarcely used as a monitoring tool by local environmental agencies in Argentina. Here, we review the literature to analyze the use of ecosystem health indicators in freshwaters from Argentina. We found 91 scientific articles relating to the use of ecological indices to assess the impact of different environmental stressors in aquatic environments published between 1996 and 2019. We generated Google Earth map where we deployed the sampling sites and type of indices reported by each article. As biological indices were the most used, we also surveyed bioindication experts to gather information on their application. We found that most studies were concentrated mainly in Pampas (34%), Dry Chaco (20%), Espinal (12%), and Patagonian Steppe (10%) ecoregions. Biological indices (mainly with invertebrates) were more used than geomorphological or physico-chemical indices. Indices resulted useful to evaluate the impact of stressors in 63% of cases, being land use the most studied stressor. However, sampling design varied greatly among studies, making their comparison difficult. The information compiled here could help to the design of monitoring protocols, the adoption of regional indices, and the creation of a national inventory of ecosystem health status, which are mandatory to propose well-grounded conservation and management policies for freshwaters in Argentina.

Characterizing ecological interaction networks to support risk assessment in classical biological control of weeds

A key element in weed biological control is the selection of a biological control agent that minimizes the risks of non-target attack and indirect effects on the recipient community. Network ecology is a promising approach that could help decipher tritrophic interactions in both the native and the invaded ranges, to complement quarantine-based host-specificity tests and gain insights on potential interactions of biological control agents. This review highlights practical questions addressed by networks, including 1) biological control agent selection, based on specialization indices, 2) risk assessment of biological control agent release into a novel environment, via particular patterns of association such as apparent competition between agent(s) and native herbivore(s), 3) network comparisons through structural metrics, 4) potential of network modelling and 5) limits of network construction methods.

Size matters in regulating the biodiversity of tropical forest soils

Tropical forests have long fascinated ecologists, inspiring a plethora of research into the mechanisms regulating their immense biodiversity, which originally captured the interests of early natural historians and explorers, and that still persists to this day. A new focus of this research emerged in the early 2000s highlighting the potential role of neutral (stochastic) processes in regulating the composition and diversity of tropical forest communities, and thus the maintenance of a large portion of global biodiversity (Hubbell, ). This strictly contrasted the long-held belief that communities assembled via the sorting of species (and their abundances) via a deterministic response to local abiotic and biotic environmental conditions, reflecting the niche of each species (Leibold & McPeek, ). Yet, it is unlikely that the assembly of any community is solely governed by either stochastic or deterministic processes, but instead a combination of both. However, whether deterministic processes via niche-based environmental sorting of species, or stochastic processes reflecting pattens of dispersal limitation, neutral effects and ecological drift dominate is often unclear. This prompts questions as to whether the relative influence of one process over another is dependent on the scale (spatial or temporal) or context of the study, or specific traits of the taxa under investigation (e.g., body size). In a From the Cover paper in this issue of Molecular Ecology, Zinger et al. () tackle all these issues and show, among other things, that for soil microbes and mesofauna from tropical forests, the relative contribution of stochastic and deterministic processes in assembling their communities is strongly dependent on the body size or the studied taxa.

Linking Soil Fungal Generality to Tree Richness in Young Subtropical Chinese Forests

Soil fungi are a highly diverse group of microorganisms that provide many ecosystem services. The mechanisms of soil fungal community assembly must therefore be understood to reliably predict how global changes such as climate warming and biodiversity loss will affect ecosystem functioning. To this end, we assessed fungal communities in experimental subtropical forests by pyrosequencing of the internal transcribed spacer 2 (ITS2) region, and constructed tree-fungal bipartite networks based on the co-occurrence of fungal operational taxonomic units (OTUs) and tree species. The characteristics of the networks and the observed degree of fungal specialization were then analyzed in relation to the level of tree species diversity. Unexpectedly, plots containing two tree species had higher network connectance and fungal generality values than those with higher tree diversity. Most of the frequent fungal OTUs were saprotrophs. The degree of fungal specialization was highest in tree monocultures. Ectomycorrhizal fungi had higher specialization coefficients than saprotrophic, arbuscular mycorrhizal, and plant pathogenic fungi. High tree species diversity plots with 4 to 16 different tree species sustained the greatest number of fungal species, which is assumed to be beneficial for ecosystem services because it leads to more effective resource exploitation and greater resilience due to functional redundancy.

Entomology in the 21st Century: Tackling Insect Invasions, Promoting Advancements in Technology, and Using Effective Science Communication-2018 Student Debates

The 2018 student debates of the Entomological Society of America were held at the Joint Annual Meeting for the Entomological Societies of America, Canada, and British Columbia in Vancouver, BC. Three unbiased introductory speakers and six debate teams discussed and debated topics under the theme 'Entomology in the 21st Century: Tackling Insect Invasions, Promoting Advancements in Technology, and Using Effective Science Communication'. This year's debate topics included: 1) What is the most harmful invasive insect species in the world? 2) How can scientists diffuse the stigma or scare factor surrounding issues that become controversial such as genetically modified organisms, agricultural biotechnological developments, or pesticide chemicals? 3) What new/emerging technologies have the potential to revolutionize entomology (other than Clustered Regularly Interspaced Short Palindromic Repeats)? Introductory speakers and debate teams spent approximately 9 mo preparing their statements and arguments and had the opportunity to share this at the Joint Annual Meeting with an engaged audience.

Adaptive Networks for Restoration Ecology

The urgent need to restore biodiversity and ecosystem functioning challenges ecology as a predictive science. Restoration ecology would benefit from evolutionary principles embedded within a framework that combines adaptive network models and the phylogenetic structure of ecological interactions. Adaptive network models capture feedbacks between trait evolution, species abundances, and interactions to explain resilience and functional diversity within communities. Phylogenetically-structured network data, increasingly available via next-generation sequencing, inform constraints affecting interaction rewiring. Combined, these approaches can predict eco-evolutionary changes triggered by community manipulation practices, such as translocations and eradications of invasive species. We discuss theoretical and methodological opportunities to bridge network models and data from restoration projects and propose how this can be applied to the functional restoration of ecological interactions.