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Soil microbiomes are extremely complex, with dense networks of interconnected microbial species underpinning vital functions for the ecosystem. In advanced agricultural research, rhizosphere microbiome engineering is gaining much attention, as the microbial community has been acknowledged to be a crucial partner of associated plants for their health fitness and yield. However, single or combined effects of a wide range of soil biotic and abiotic factors impact the success of engineered microbiomes, as these microbial communities exhibit uneven structural and functional networks in diverse soil conditions. Therefore, once a deep understanding of major influential factors and corresponding microbial responses is developed, the microbiome can be more effectively manipulated and optimized for cropping benefits. In this mini-review, we propose the concept of a microbiome-mediated smart agriculture system (MiMSAS). We summarize some of the advanced strategies for engineering the rhizosphere microbiome to withstand the stresses imposed by dominant abiotic and biotic factors. This work will help the scientific community gain more clarity about engineered microbiome technologies for increasing crop productivity and environmental sustainability.Key points• Individual or combined effects of soil biotic and abiotic variables hamper the implementation of engineered microbiome technologies in the field.• As a traditional approach, reduced-tillage practices coinciding with biofertilization can promote a relatively stable functional microbiome.• Increasing the complexity and efficiency of the synthetic microbiome is one way to improve its field-application success rate.• Plant genome editing/engineering is a promising approach for recruiting desired microbiomes for agricultural benefit.

Plants synthesize a vast array of specialized metabolites that primarily contribute to their defense and survival under adverse conditions. Many of the specialized metabolites have therapeutic values as drugs. Biosynthesis of specialized metabolites is affected by environmental factors including light, temperature, drought, salinity, and nutrients, as well as pathogens and insects. These environmental factors trigger a myriad of changes in gene expression at the transcriptional and posttranscriptional levels. The dynamic changes in gene expression are mediated by several regulatory proteins that perceive and transduce the signals, leading to up- or down-regulation of the metabolic pathways. Exploring the environmental effects and related signal cascades is a strategy in metabolic engineering to produce valuable specialized metabolites. However, mechanistic studies on environmental factors affecting specialized metabolism are limited. The medicinal plant Catharanthus roseus (Madagascar periwinkle) is an important source of bioactive terpenoid indole alkaloids (TIAs), including the anticancer therapeutics vinblastine and vincristine. The emerging picture shows that various environmental factors significantly alter TIA accumulation by affecting the expression of regulatory and enzyme-encoding genes in the pathway. Compared to our understanding of the TIA pathway in response to the phytohormone jasmonate, the impacts of environmental factors on TIA biosynthesis are insufficiently studied and discussed. This review thus focuses on these aspects and discusses possible strategies for metabolic engineering of TIA biosynthesis.Purpose of workCatharanthus roseus is a rich source of bioactive terpenoid indole alkaloids (TIAs). The objective of this work is to present a comprehensive account of the influence of various biotic and abiotic factors on TIA biosynthesis and to discuss possible strategies to enhance TIA production through metabolic engineering.

Escalated production of plastic, their worldwide distribution and persistent nature finally results into their environmental accumulation causing severe threats to the ecological environment and biotic health. Thus, development of suitable measurements for environmental remediation of plastic may be an urgent issue in this plastic age. Some recent reviews have categorized the microbial species able to degrade different plastic polymers and the different factors effecting bio-degradation of plastic are poorly understood. This review comprehensively discusses bio-degradation of traditional and biodegradable plastic polymers both in natural and biological environment (gut microbes and fungi) to understand different factors regulating their degradation, and also shows how degradation of plastic polymers under abiotic factors influence subsequent biological degradation. Different physicochemical modifications like - breaking large polymers into small fragments by pre-treatment, functional groups enrichment, identifying potent microbial species (consortia) and engineering microbial enzymes might be crucial for bio-degradations of plastic. Effects of micro/nanoplastic and other chemical intermediates, formed during the bio-degradation of plastic, on species composition, abundance, growth, metabolism and enzymatic systems of microbes involved in the bio-degradation of plastic should be determined in future research.

Environmental stochasticity in abiotic factors is inherent to ecosystems and is exacerbated by global change. However, experimental protocols typically cancel this factor by using cyclic or constant conditions, limiting the study of environmental variations. This simplification highlights the need for better methodological tools to control fluctuating environmental variables. We present here a guidance and solution for generating and implementing stochastic environmental conditions through our Raspberry Pi System for environmental Stochasticity (PiStoch). This low‐cost, low‐tech and scalable method for mesocosm experiments also has the potential to replicate any other form of variability, including cyclic patterns. This system successfully reproduced stochastic time series in temperature and oxygen manipulation experiments. Testing with two biological case studies (macrophyte biomass and freshwater fish oxygen consumption), it demonstrated that thermal stochasticity had stronger effects than mean temperature, highlighting the importance of studying fluctuating conditions. Developing accessible methods to study organismal responses to environmental stochasticity is essential for improving the realism of laboratory experiments and enhancing the accuracy of physiological and ecological predictions. Résumé La stochasticité environnementale est inhérente aux écosystèmes et exacerbée par le changement climatique actuel. Cependant, les protocoles expérimentaux en laboratoire ne prennent pas en compte ce paramètre n’utilisant que des conditions cycliques ou constantes, limitant ainsi la connaissance des effets des variations environnementales sur le vivant. Cette simplification expérimentale souligne la nécessité de disposer d’outils méthodologiques performants pour contrôler les fluctuations des variables environnementales en laboratoire. Nous présentons ici un appareillage accompagné d’un guide pour générer et mettre en œuvre des conditions environnementales stochastiques grâce à un système appelé PiStoch et basé sur un Raspberry Pi. Cette méthode peu coûteuse, simple à mettre en place et évolutive permet de reproduire toute forme de variabilité au sein de mésocosmes. Ce système a reproduit avec succès des séries temporelles stochastiques lors d’expériences sur des variations de température et d’oxygène. Testé sur deux modèles biologiques différents (macrophytes et poissons d’eau douce), il a démontré qu’à moyenne égale, la stochasticité thermique avait des effets plus importants que la température constante, soulignant l’importance d’étudier ces conditions fluctuantes. Le développement de méthodes accessibles pour étudier les réponses des organismes à la stochasticité environnementale est essentiel pour améliorer le réalisme des expériences en laboratoire et accroître la précision des prédictions physiologiques et écologiques.

Slope aspect can cause environmental heterogeneity over relatively short distances, which in turn affects plant distribution, community structure, and ecosystem function. However, the response and adaptation strategies of plants to slope aspects via regulating their physiological and morphological properties still remain poorly understood, especially in alpine ecosystems. Here, we selected four common species, including Bistorta macrophylla , Bistorta vivipara , Cremanthodium discoideum , and Deschampsia littoralis , to test how biomass allocation and functional traits of height, individual leaf area, individual leaf mass, and specific leaf area (SLA) respond to variation in slope aspect in the Minshan Mountain, eastern Tibetan Plateau. We found that the slope aspect affected SLA and stem, flower mass fraction with higher values at southwest slope aspect, which is potentially related to light environment. The low-temperature environment caused by the slope aspect facilitates the accumulation of root biomass especially at the northeast slope aspect. Cremanthodium discoideum and D. littoralis invested more in belowground biomass in southeast and southwest slope aspects, although a large number of significant isometric allocations were found in B. macrophylla and B. vivipara . Finally, we found that both biotic and abiotic factors are responsible for the variation in total biomass with contrasting effects across different species. These results suggest that slope aspect, as an important topographic variable, strongly influences plant survival, growth, and propagation. Therefore, habitat heterogeneity stemming from topographic factors (slope aspect) can prevent biotic homogenization and thus contribute to the improvement of diverse ecosystem functioning.

Oxygen in its molecular state O₂, is essential for many metabolic processes that are vital to aerobic life. Aerobic organisms cannot exist without oxygen, which nevertheless is inherently dangerous to their lives. Like all aerobic organisms, fish are also susceptible to the effects of reactive oxygen and have inherent and effective antioxidant defenses that are well described in the literature. This review investigates the influence of different biotic and abiotic factors (age, phylogenetic position, feeding behavior, environmental factors, oxygen, temperature, presence of xenobiotics) on antioxidant defenses in fish. Studies of antioxidant activity in fish open a number of novel research lines providing greater knowledge of fish physiology, which will benefit various aspects of fish farming and artificial production.

Broad-leaved deciduous forests in the transitional region from temperate to subtropical climate in China exhibit a diverse assemblage of species. The effects of potential biotic and abiotic factors on forest species diversity are currently of great interest. Here, we quantified the diversity of woody plant species across vertical strata in a fully recorded 25-ha permanent forest dynamics plot (500 × 500 m) in the Mts. Qinling of China using 4 indices: Pielou evenness index ( J SW ), Shannon entropy ( H ), species richness ( S ), and species abundance. Analysis of multivariate linear regression was employed to compare the influences of potential biological, topography, and soil variables on the alpha diversity for each of the 625 sub-plot (20 × 20 m) in the canopy layer, substory layer, and understory layer. The results displayed that the indices of the alpha diversity significantly varied among different forest vertical strata and they were mostly and significantly related to the DBH structure variable, soil available phosphorus (P), and altitude. Despite vertical strata of the studied forest, biological, topographic, and soil factors jointly showed reasonably strong explanatory power for species diversity. More than 12% of the variations of the alpha diversity in canopy layer and 16% in substory layer as well as 8% in understory layer could be collectively explained by biological, topographic, and soil factors. Our findings can contribute to the understanding of how environmental and biological factors interact to affect species diversity and thus are of great implication for the preservation of forest species diversity.

Understanding how geomorphic landscape features affect physical habitat conditions is essential for predicting if such geomorphic landscape features may act as conduits facilitating invasive species expansion in coastal ecosystems. Although the effects of various abiotic and biotic factors on plant invasion in salt marshes have been well studied, little is known about the impact of tidal channels on plant invasion. Here, we examined the effects of bottom-up determinants on the lateral expansion of Spartina alterniflora in tidal channel margins of different elevational marsh zones: the low, middle and high marsh, in the Yellow River Delta, China. Field observations and experiments showed that the microhabitats of tidal channel margins are characterized by relatively low soil salinity and high inundation, which significantly facilitated the establishment, growth, colonization and sexual reproduction of S. alterniflora. Moreover, the facilitating effect of tidal channel margins on plant landward invasion appeared more sensitive in middle and high marshes compared with the low marshes. High propagule pressure combined with suitable physical conditions of the structural microhabitats formed within tidal channels potentially promoted the rapid expansion of S. alterniflora along the tidal channel margins. Based on these results, a conceptual model was built illustrating the lateral expansion mechanisms of the invasive plant mediated by tidal channels. These results highlight the importance of tidal channel-mediated gradients in bottom-up abiotic and biotic-dispersal factors in facilitating the expansion of coastal invasive plants. For wetlands management, our results imply that geomorphic landscape features should be incorporated into ecological management and risk assessment of invasive plants.

Background The microbiota in fish external mucus is mainly known for having a role in homeostasis and protection against pathogens, but recent evidence suggests it is also involved in the host-specificity of some ectoparasites. In this study, we investigated the influence of seasonality and environmental factors on both fish external microbiota and monogenean gill ectoparasites abundance and diversity and assessed the level of covariations between monogenean and bacterial communities across seasons. To do so, we assessed skin and gill microbiota of two sparid species, Oblada melanura and Diplodus annularis , over a year and collected their specific monogenean ectoparasites belonging to the Lamellodiscus genus. Results Our results revealed that diversity and structure of skin and gill mucus microbiota were strongly affected by seasonality, mainly by the variations of temperature, with specific fish-associated bacterial taxa for each season. The diversity and abundance of parasites were also influenced by seasonality, with the abundance of some Lamellodiscus species significantly correlated to temperature. Numerous positive and negative correlations between the abundance of given bacterial genera and Lamellodiscus species were observed throughout the year, suggesting their differential interaction across seasons. Conclusions The present study is one of the first to demonstrate the influence of seasonality and related abiotic factors on fish external microbiota over a year. We further identified potential interactions between gill microbiota and parasite occurrence in wild fish populations, improving current knowledge and understanding of the establishment of host-specificity.

Key messageKorean pine trees expressed significant crown displacement. Nearest neighbor competition had the largest effect on the crown displacement compared to the slope direction and mean direction of wind.The crown displacement of individual trees exhibits an adaptive response driven by neighbors, but it can also be the result of wind force and slope effects. In our research, we focused on the crown displacement of planted Korean pine trees in northeast China. A total of 51 trees aged 8–56 years were destructively harvested to measure branch attributes. The gravity centers of the upper, lower and entire crown were calculated. The Markov chain Monte Carlo (MCMC) algorithm, generalized mixed effects model, and circular statistics were used to determine the response of crown displacement to biotic and abiotic factors. The results showed that the dominant tree had the largest absolute crown displacement, and the suppressed tree expressed the largest relative crown displacement. The lower crown showed more apparent crown displacement than the upper crown. The Korean pine was displaced in a northeastern direction. Nearest neighbor competition had the largest effect on the crown displacement compared to the slope direction. Slope direction had a slightly larger effect than the mean direction of wind. The crown displacement for the lower crown was more affected by the interaction of the wind, slope and neighbor competition than the upper crown. No relationship between crown displacement and stem eccentricity for the planted Korean pine was detected.