2770100x, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/mlf2.12054 by Readcube (Labtiva Inc.), Wiley Online Library on [18/01/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License PERSPECTIVE Ecosystem Microbiome Science Yong‐Guan Zhu1,2,* , Dong Zhu2, Matthias C. Rillig3,4, Yunfeng Yang5 , Haiyan Chu6, Qing‐Lin Chen7, Josep Penuelas8,9,*, Hui‐Ling Cui2, and Michael Gillings10,* Edited by Qiang He, University of Tennessee, Knoxville, USA; Received September 4, 2022; Accepted December 15, 2022; Published online January 07, 2023 Abstract The microbiome contributes to multiple ecosystem functions and services through its interactions with a complex environment and other organisms. To date, however, most microbiome studies have been carried out on individual hosts or particular environmental compartments. This greatly limits a comprehensive understanding of the processes and functions performed by the microbiome and its dynamics at an ecosystem level. We propose that the theory and tools of ecosystem ecology be used to investigate the connectivity of microorganisms and their interactions with the biotic and abiotic environment within entire ecosystems and to examine their contributions to ecosystem services. Impacts of natural and anthropogenic stressors on ecosystems will likely cause cascading effects on the microbiome and lead to unpredictable outcomes, such as outbreaks of emerging infectious diseases or changes in mutualistic interactions. Despite enormous advances in microbial ecology, we are yet to study microbiomes of ecosystems as a whole. Doing so would establish a new framework for microbiome study: Ecosystem Microbiome Science. The advent and application of molecular and genomic technologies, together with data science and modeling, will accelerate progress in this field. Keywords: dynamics; ecosystem; global change; interactions; microbiome INTRODUCTION Human prosperity relies on ecosystem functioning including changing technology for microbial ecology4,5. The Raman production of food, fiber, and fuel. Ecosystem ecology pri- spectrum of a cell is a unique fingerprint of its chemical marily addresses the exchange of energy and materials be- composition and contains information on its taxonomic tween organisms within an ecosystem and with the abiotic identity and physiological state5. More importantly, this environment within which an ecosystem is functioning. It technique is nondestructive and allows downstream anal- studies the interactions between organisms and their yses such as sorting, sequencing, or cultivation of taxa of physical environment as an integrated system1. Such interest6,7. All these techniques have rapidly expanded, in- studies have dealt primarily with macro‐organisms and pre- creasing the realization that microorganisms are playing a dominantly focused on vascular plants. With the advent of central part of all ecosystem ecological functions and serv- modern genomic and molecular techniques, such as the ices (Figure 1). On the one hand, microbes influence plant second‐ and third‐generation sequencing technologies as performance and primary production, mediating tolerance to well as the metabolomics, many fascinating discoveries were biotic stresses and fostering nutrient acquisition, and on the made on microbial diversity and their interactions. Microbial other hand, they play central roles in virtually all bio- community structures and basic patterns of the composition geochemical processes8,9. These processes occur simulta- and dynamics of microbial communities have now become neously and are often colocated, and yet, are typically feasible even at global scales2,3. In addition to the omics studied in isolation. For example, there are many studies on techniques, next‐generation physiology approaches such as the effects of the soil microbiome on plant performance, but Raman microspectroscopy represents a potentially game‐ it is unclear how other microbial processes at the ecosystem 1 Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China. 2State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco‐environmental Sciences, Chinese Academy of Sciences, Beijing, China. 3Institute of Biology, Freie Universität Berlin, Berlin, Germany. 4Berlin‐ Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany. 5State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China. 6State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China. 7Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia. 8CSIC, Global Ecology Unit CREAF‐CSIC‐UAB, Bellaterra, Catalonia, Spain. 9CREAF, Cerdanyola del Vallès, Catalonia, Spain. 10ARC Centre of Excellence for Synthetic Biology, and Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia. * Correspondence: Yong‐Guan Zhu, ygzhu@rcees.ac.cn; Josep Penuelas, josep.penuelas@uab.cat; Michael Gillings, michael.gillings@mq.edu.au DOI: 10.1002/mlf2.12054 This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Month 2023 | Volume 1 | Issue 4 | 1–9 wileyonlinelibrary.com/journal/mLife 2770100x, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/mlf2.12054 by Readcube (Labtiva Inc.), Wiley Online Library on [18/01/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 2 Figure 1. The concept of ecosystem microbiomes and a technique map to briefly show how to study microbial genomes and functions in whole ecosystems. In general, omics methods could provide taxonomic and metabolic information at the community level. The recently developed functional Raman spectroscopy‐based single‐cell technology as a next‐generation physiology method could provide information on microbiome function at the single‐cell level. 2770100x, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/mlf2.12054 by Readcube (Labtiva Inc.), Wiley Online Library on [18/01/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 3 level affect feedbacks on plant growth and vice versa. Since spatiotemporal dynamics of microbiomes at an ecosystem microbial activities are interconnected, biological mecha- level, and we need to study the connectivity of microbiomes nisms operating at one level of biological organization can between different ecosystem components. affect functioning at higher organizational levels10. As a re- Assessing the distribution of microbiomes within an sult, ecosystem processes across entire microbiomes should ecosystem requires comprehensive sampling and se- be examined simultaneously across organizational levels to quencing, both spatially and temporally11. By taking sam- uncover intricate linkages and feedbacks. This is the essence ples from highly accessed urban surfaces and parks in New of what we are calling Ecosystem Microbiome Science—the York City, Afshinnekoo et al.12 found that 1688 bacterial, simultaneous examination of microbial genomes, functions, viral, archaeal, and eukaryotic taxa inhabited the area. The and their interactions in whole ecosystems. microbiota were enriched for genera associated with skin, The term microbiome refers to all microbes, including showing transfer of human microbiota into the environ- archaea, bacteria, fungi, protists, and viruses, that are as- ment. They also showed that bacterial signatures can sociated with an animal or plant host or occupy an environ- match the history of an extreme climate event, such as the mental compartment such as soil and water. With the advent appearance of marine‐associated bacteria in a hurricane‐ of molecular and genomic tools and data science, it is now flooded station. Using bioinformatics and machine learning, much easier to capture and understand the complexity of microbial genomics data can generate fingerprints of cities microbial systems. Microbiome studies often examine the based on urban microbiome compositions13. Such studies composition and function of the microbiome in individual and data sets may shed light on the spread of human‐ hosts or in a sample taken from a particular environment. derived microbes and help develop surveillance tools for However, due to the lack of systematic thinking and accurate human infectious diseases worldwide. microbial tracing technology, microbiome studies are rarely The “terroir” concept used in wine‐making14 is another integrated with measurements of the pools and fluxes of example of the role of microbiomes within an ecosystem15. matter and energy in ecosystems. Similarly, the spatial and In a comprehensive study of the soil and vine microbiome, temporal dynamics of microbiomes is rarely examined. Zarraonaindia et al.16 found that while vine‐associated micro- Therefore, we define the ecosystem microbiome as the biomes were affected by an array of diverse factors, the ma- consortia of microbes that reside within a given ecosystem jority of organ‐associated microbial taxa originated from soil (e.g., tropical forest, human body, or paddy field). Ecosystem and their distribution reflected both the impact of local bio- Microbiome Science addresses the interactions between geographic factors and how the vineyard was managed. This microbiomes and the environment and the movement and suggests that soil serves as a major source of vine‐associated functions of microbiomes within an integrated ecosystem. bacteria and influences the grape‐associated microbiome im- Based on previous results and current knowledge, four portant for wine‐making. We can further infer that signature general questions for Ecosystem Microbiome Science ecosystem microbiomes (i.e., soil‐ and vine‐associated micro- studies will be discussed in the paper: (1) distribution and biomes) and biogeographic factors affecting them may con- movement of microbiomes within an integrated ecosystem; tribute to a regional terroir of the wine. Beyond this “terroir” (2) connectivity of ecosystem microbiomes; (3) temporal dy- example, the plant and soil microbiome will impact postharvest namics of ecosystem microbiomes; and (4) applications of processes for many crops. The influence of the ecosystem Ecosystem Microbiome Science. microbiome likely extends far into the agri‐food chain; for ex- ample, soil microbiome elements may determine food storage DISTRIBUTION AND MOVEMENT OF traits or influence food nutritional value14. MICROBIOMES WITHIN AN INTEGRATED In ecosystems, microbes can move as entire commun- ECOSYSTEM ities17, not just as individual species or phylotypes, the latter Traditionally, characterization of an ecosystem is achieved by movement being well captured in current meta‐community the analysis of the fluxes of energy and materials through theory18. Since parts of the environment are colonized by organisms and the physical environment and by cataloguing microbes, and these parts can be moved by a range of biodiversity (mostly of macroorganisms) within an eco- processes (including gravity and water flows), the asso- system. However, we believe that such a characterization is ciated microbial communities are moved as well. The en- becoming increasingly insufficient for understanding the counter and mixing of previously separated microbial properties and functions of an ecosystem. Although there are communities is community coalescence18,19. This concept numerous studies on the soil microbiome and emerging includes the merging of entire communities and their envi- studies on the plant microbiome, we still know little about ronments (e.g., in aquatic environments, the mixing of saline these microbiomes at the ecosystem level. For example, do water and freshwater). An immediately obvious example is different ecosystems have signature microbiomes/microbial litterfall, whereby the leaf microbiome encounters the soil taxa/keystone species? How do ecosystems differ in terms microbiome on a massive scale. Theory and empirical evi- of microbial connectivity among different components? And dence also suggests that communities, upon coalescence, does it matter? What are the driving forces of microbiome can maintain a certain degree of coherence, highlighting exchange between different components of an ecosystem? the importance of studying such microbiome fluxes at To answer all these questions, we should analyze the the ecosystem scale, incorporating the microbiome 2770100x, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/mlf2.12054 by Readcube (Labtiva Inc.), Wiley Online Library on [18/01/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 4 endmembers (i.e., pools), fluxes, and resulting community webs, animals and plants, are always colonized by micro- coalescence phenomena20. organisms that play important roles in the health and bio- geochemistry of their hosts23,24. Consequently, while these microorganisms are tightly connected to the food web in an CONNECTIVITY OF ECOSYSTEM integrated ecosystem25, they are largely ignored, except for MICROBIOME their roles as degraders. Trophic linkages of microbiomes within an Different organisms have distinct microbiomes, sug- integrated ecosystem gesting that these microorganisms play different roles in Food webs are depictions of feeding relationships with an ecosystems. The specificity of these interactions means that ecosystem (Figure 2). Trophic relationships regulate key extinction of hosts could potentially lead to a decline in the ecological processes such as the flow of materials and en- overall microbial diversity and associated functions, even ergy21,22. The most frequently studied components of food before these microorganisms are discovered. It has been Figure 2. The connectivity of the ecosystem microbiome. Trophic regulation including bottom‐up and top‐down control of the ecosystem microbiome is the key ecological process that links to the flow of materials and energy in the ecosystem. 2770100x, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/mlf2.12054 by Readcube (Labtiva Inc.), Wiley Online Library on [18/01/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 5 suggested that the transfer of microorganisms in the food cascading effects could magnify the impact of top predators, web plays an important role in the health of animals and affecting microbiomes of lower trophic levels in the food web plants in an integrated ecosystem26. The microbiome of or- by altering the behavior, morphology, and population size of ganisms at higher trophic levels can be a subset of those at organisms at other trophic levels. Effects of one predator lower trophic levels in the food web and in the environment27. extinction on the diversity of a microbiome in an ecosystem This suggests that organisms higher up the food chain can might be reduced due to trophic redundancy. Although re- acquire their microbiome from organisms lower down. lated studies regarding trophic redundancy in animal micro- However, it is not fully understood which microbes can be biomes are scarce, some evidence has been emerging from transferred between organisms at different trophic levels. community ecology. Construction of communities with four Broadly, the trophic dynamics of the microbiome is con- trophic levels38 revealed that trophic redundancy could de- trolled by two biotic factors within ecosystems: diet‐driven crease the vulnerability of ecosystems to extinction of (bottom‐up) and consumer regulation (top‐down). Effects of predators due to biodiversity loss38. food and predators on the structure and function of food web have been widely studied, such as predator control of nu- TEMPORAL DYNAMICS OF THE trient cycling28. As expected, they have direct/indirect effects ECOSYSTEM MICROBIOME on the structure and function of microbiomes in the The dynamic interplay between organisms and resource supply food web. determines succession in ecosystems, these being directional changes in structure and function. Succession has been un- derstood for many years as an ordered sequence of commun- Bottom‐up and top‐down control of the ities building to a climax community or as a predicted community ecosystem microbiome composition dictated by the abiotic and biotic environmental Diet has a vital influence on the composition and structure of an conditions within the biome39. The structure and functioning of individual animal microbiome29,30. For example, an antibiotic‐ ecosystem microbiomes also change over time in primary suc- treated diets could not only alter the gut microbiome of cattle cessions (in newly created habitats) and in secondary succes- but could also affect the microbiome of nontarget animals such sions (with survival of residuals, e.g., after a disturbance such as as dung beetles and affect the ecosystem services that they fire, drought, typhoon, or landslide). For example, de Araujo provide31. In addition, prey could alter the microbial community et al.40 investigated the soil microbiome along a gradient of structure of a predator32. In a zebrafish experiment, the mi- Cerrado savannah, including grass, grass and shrub, shrub and crobiome could be dispersed between species33, suggesting tree, and tree‐dominated zones. They found that complexity of that a change of community structure in the prey might affect the microbiome increased towards the tree‐dominated climax the dynamics of the microbiome in the whole ecosystem. and that the highly interconnected microbiome played a vital role Moreover, food could act as a vector for microbiome transfer in in maintaining ecosystem performance. Moreover, microbial the food web. In a soil–plant–caterpillar study, soil microbiomes assembly could be shifted during the succession, for example, could be transmitted into insect microbiomes via ingested the soil microbial community composition was initially governed plants. Movement of insects could carry acquired micro- by stochasticity, but there was a progressive increase in de- organisms into other organisms’ microbiomes34. By under- terministic selection as succession proceeded in a salt mash standing microbiome dynamics at the ecosystem level, we chronosequence spanning 105 years41. Despite these efforts, could better reveal the effects of diet on ecosystem processes our understanding of succession of microbiomes during eco- and functions. system development is still in its infancy, especially at an eco- Organisms at higher trophic levels directly alter the mi- system level, and it is not clear if the climax communities are the crobiome of prey via predation. There are two scenarios re- same for the microbiomes in similar compartments of different garding the impact of predation on the microbiomes of prey. ecosystems. Future studies will be needed to go beyond the soil First, if the prey is ingested or dead, the niche associated microbiome, to include the microbiome in other ecosystem with prey will shift or predation will produce an unrecognized compartments. Plant roots, leaf surfaces, and soil invertebrates route of bacterial transmission. In a snail‐grazed mesocosm are all likely to have unique climax communities that interact with study, grazing by snails increased fungal community heter- soil, water, and atmospheric microbiomes. Understanding con- ogeneity in the phyllosphere and could lead to ecosystem nectivity, cosuccession, and coevolution of microbiomes across fragmentation35. A recent field study also indicated that in- ecosystems will help us manage their influence on ecosystem sect herbivory could alter endophytic bacterial diversity functioning. patterns within a native plant host36. Second, if the prey is Microbiomes can exist in alternative stable states, similar to not ingested, its microbiome may also be altered under the alternative vegetation landscapes, such as savannah versus for- pressure of predation. Predation stress could reduce species ests42. These alternative states can depend on the order of richness and alter the metabolic repertoire of bacteria in the species arrival to the new environment (priority effects) or on the microbiome of prey37. This is likely because prey can alter selective removal of keystone species. Once established, com- their behavior, diet, and habitat to avoid being captured. munities have positive feedbacks that can build resistance and Interactions between species could alter the effects resilience to change in response to further disturbance. The of predators on ecosystem microbiomes. For example, changes in microbiome communities depend on predisturbance 2770100x, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/mlf2.12054 by Readcube (Labtiva Inc.), Wiley Online Library on [18/01/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 6 composition, source pools for recolonization postdisturbance, as Bifidobacterium adolescentis and Bacillus badius, while and type of disturbance, but they always occur due to the dis- stimulating pathogenic bacteria such as Salmonella enter- appearance of some species and the appearance of others. itidis and Clostridium perfringens58. With rapid global Disappearances may arise from local extinction or emigration out warming, permafrost thaw and glacial retreat in polar and of the area, and appearances may arise from speciation or im- alpine regions could release pathogens and viruses that have migration into the area. The best model for these phenomena is been trapped and preserved for tens to hundreds of thou- the human microbiome and its effect on health43, but similar sands of years. Pithovirus sibericum, Mollivirus sibericum, effects must be happening in all other organisms whose micro- and Pandoraviruses are some of the 30,000‐year‐old icosa- biota are affected by human activity. hedral DNA viruses isolated from Siberian permafrost. These Species turnover can be high among microbes, partic- are capable of infecting unicellular protists such as Acan- ularly in bacteria, which can speciate rapidly due to shorter thamoeba, suggesting that global warming or industrial ex- generation time and horizontal gene transfer (HGT)17,44. It has ploitation of circumpolar regions might lead to unexpected been suggested that HGT could accelerate bacterial adap- threats to human or animal health59,60. Noroviruses and co- tation by vectoring ecologically important traits or reducing ronaviruses often adsorb readily to soils and remain viable selective constraints on the spread of genetic variation45,46. from days to years61–63, which poses a previously overlooked Therefore, HGT is an evolutionary force that facilitates the health risk. In contrast, pathogenic organisms such as Sal- spread of nonselected genetic variation and expands the monella enterica ssp. and enterica serovar Typhimurium‐lux adaptive ability of microbial populations, which will sub- can leach through soils, suggesting that groundwater con- stantially impact the ecosystem microbiome and lead to new tamination from vertical movement of pathogens is also a uncertainties in terms of the use of traditional ecological potential risk61. theories and models to explore microbial succession and A comprehensive understanding of the human health risk community assembly at the ecosystem level47,48. associated with environmental microbiomes will require a holistic view that emphasizes interactions among members within microbiomes, as well as their coevolution with their APPLICATIONS OF ECOSYSTEM neighbors and hosts. As viruses are important reservoirs of MICROBIOME SCIENCE antibiotic resistance genes in the environment64, the practice Links between the ecosystem microbiome and of using antibiotics to treat complications of viral infection emerging infectious diseases (EIDs) should be carefully reconsidered. To wholly appreciate the Individuals disperse more than 300 million bacterial cells into complex level of interspecies interaction, it is necessary to the environment on a daily basis, with human skin being the use the full arsenal of current technologies. It is also im- dominant contributor to the microbiome of built environ- portant to carefully design longitudinal studies associated ments49. However, industrialization and urbanization have with simplified, pragmatic sampling strategies. resulted in a substantially less diverse human microbiome50, while anthropogenically induced changes, such as global warming and eutrophication, have also reduced environ- Conservation of the ecosystem microbiome: mental microbial diversity51,52. As a consequence, many Microbial seed banks beneficial microbes needed for health are disappearing53. Humans are now the greatest evolutionary force on the Perturbations to the human microbiome are increasingly planet65 (Figure 3). Our activities significantly alter ecosys- being associated with allergies, cancer, type II diabetes, tems and have precipitated the 6th Mass Extinction66,67. depression, vascular, inflammatory, and neurological and Microorganisms are not immune to these effects and are cognitive disease. Such conditions can accelerate the like- likely also going extinct68,69. The best evidence for potential lihood and impact of global pandemics. extinctions comes from studies of the human microbiota, EIDs are threatening global health and stability. Many EIDs where significant numbers of taxa are known to be missing are deeply rooted in the environment, and changes in eco- from urbanized populations43. The loss of these microbes system microbiomes play a crucial role in their emergence. may promote the spread of antibiotic resistance, reduce the The cascading effects of human‐induced changes on EIDs ability of host to resist epidemics, and may also affect host have been widely observed, such as land conversion and development. Therefore, the potential for microbial extinction spillover of pathogens through biodiversity loss and changes events has led to the establishment of “seed banks” of the in human–nature contact54,55. This is particularly true with human microbiota, sourced from multiple cultures, but fo- zoonoses originating from wildlife, such as COVID‐19. For cused primarily on collections from minimally disturbed tra- example, the risk of zoonotic EIDs is elevated in tropical re- ditional populations70. Other microbiome banks are being gions with high biodiversity, but experiencing land‐use established for medical, agricultural, and conservation pur- changes56. poses71,72. Cascading effects on ecosystem microbiomes are also Most data on the diversity of microbiota have been ob- caused by chemical pollution. Various chemicals are known tained from studies on humans and a few other model spe- to alter microbiomes and their metabolic capabilities57. The cies. There is, however, an increasing interest in the herbicide glyphosate can eliminate beneficial bacteria such microbiota of other organisms, including plants, birds, and 2770100x, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/mlf2.12054 by Readcube (Labtiva Inc.), Wiley Online Library on [18/01/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 7 Figure 3. Microbial cycling between humans and ecosystems. It is generally accepted that microbes are important for human health, and novel functions of the microbiome in human health and well‐being are being increasingly recognized. Therefore, there is a need to better understand the potential connections between ecosystem and human health in an ecosystem context. invertebrates, in addition to mammals73–79. This is appro- microbiota could be an essential tool for saving these hosts priate, given that microbial extinctions are likely to affect the from extinction87. microbiota of all organisms directly affected by human ac- tivity. Such studies are particularly important for terrestrial CONCLUDING REMARKS plants, since most plants form symbioses with soil micro- Microbiomes from different compartments within an eco- organisms80,81. We suspect that genes in the microbiota will system are highly connected. Their roles in mediating allow an opportunity for rapid acquisition of new phenotypes ecosystem‐level processes and functions are determined by and consequently, rapid adaptation to environmental their physiology and by their dynamic movement and inter- change82. actions with other biotic/abiotic factors in an ecosystem. We, The microbiota are also likely to influence behavior in both therefore, propose that future research should embrace the humans and in animals83,84. Conservation geneticists have entire microbiome within an integrated ecosystem to avoid been promoting the preservation of genetic diversity for fragmented views of microbiome properties, from the per- some time85. However, if microbiota are a significant source spective of both community and functional traits. We posit of phenotypic and functional diversity, we risk losing this that the tools and frameworks of ecosystem ecology can be diversity with the loss of species from the microbiota. As a applied and expanded to microbiome science, so that we consequence, calls are being made for the conservation of can better understand the links between the different com- the holobiont, that is, the macro‐organism along with its partments of ecosystems. This would revolutionize our ability resident microbiota84. Such conservation must extend to to understand and harness links and predict responses to both plants and animals86. The conservation of host species anthropogenic influences, such as EIDs. 2770100x, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/mlf2.12054 by Readcube (Labtiva Inc.), Wiley Online Library on [18/01/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 8 ACKNOWLEDGMENTS 20 Tikhonov M. Community‐level cohesion without cooperation. eLife. This study was supported financially by the National Natural 2016;5:e15747. 21 Stouffer DB, Bascompte J. Understanding food‐web persistence Science Foundation of China (Nos. 21936006 and 42021005) from local to global scales. Ecol Lett. 2010;13:154–61. and the Alliance of International Science Organizations (Grant 22 Montoya JM, Rodríguez MA, Hawkins BA. Food web complexity and No. ANSO‐PA‐2020‐18). higher‐level ecosystem services. 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