Donna Haraway and Bruno Latour

Crop diversity benefits carabid and pollinator communities in landscapes with semi‐natural habitats

Guillermo Aguilera

1. In agricultural landscapes, arthropods provide essential ecosystem services such as biological pest control and pollination. Intensified crop management practices and homogenization of landscapes have led to declines among such organisms. Semi‐natural habitats, associated with high numbers of these organisms, are increasingly lost from agricultural landscapes but diversification by increasing crop diversity has been proposed as a way to reverse observed arthropod declines and thus restore ecosystem services. However, whether or not an increase in the diversity of crop types within a landscape promotes diversity and abundances of pollinating and predaceous arthropods, and how semi‐natural habitats might modify this relationship, are not well understood.
2. To test how crop diversity and the proportion of semi‐natural habitats within a landscape are related to the diversity and abundance of beneficial arthropod communities, we collected primary data from seven studies focusing on natural enemies (carabids and spiders) and pollinators (bees and hoverflies) from 154 crop fields in Southern Sweden between 2007 and 2017.
3. Crop diversity within a 1‐km radius around each field was positively related to the Shannon diversity index of carabid and pollinator communities in landscapes rich in semi‐natural habitats. Abundances were mainly affected by the proportion of semi‐natural habitats in the landscape, with decreasing carabid and increasing pollinator numbers as the proportion of this habitat type increased. Spiders showed no response to either crop diversity or the proportion of semi‐natural habitats.
4. Synthesis and applications. We show that the joint effort of preserving semi‐natural habitats and promoting crop diversity in agricultural landscapes is necessary to enhance communities of natural enemies and pollinators. Our results suggest that increasing the diversity of crop types can contribute to the conservation of service‐providing arthropod communities, particularly if the diversification of crops targets complex landscapes with a high proportion of semi‐natural habitats. 

Effect of crop diversity on the (a) total arthropod diversity (Shannon) and the diversity of each guild (b = carabids, c = spiders, d = pollinators) in landscapes with high (black = landscape with 30% SNH) and low (red = landscape with 10% SNH) proportions semi‐natural habitats. Crop diversity and arthropod diversity are both calculated as a Shannon diversity index. Shown are fitted lines and 95% confidence intervals and p‐values for the interaction 

https://bit.ly/3kIA2Qa

.

.
SCARLET MEDUSA  

In Japan, an aging scientist works to unlock the biological secret of immortality held in the life cycle of a tiny jellyfish. At a temple in Kyoto, a Zen priest contemplates the metaphysical immortality held within a single breath.

.

THE SEEDS

By Wendell Berry

The seeds begin abstract as their species,

remote as the name on the sack

they are carried home in: Fayette Seed Company

Corner of Vine and Rose. But the sower

going forth to sow sets foot

into time to come, the seeds falling

on his own place. He has prepared a way

for his life to come to him, if it will.

Like a tree, he has given roots

to the earth, and stands free.

.

Plant–microbiome interactions: from community assembly to plant health 
Trivedi et al., 2020

Healthy plants host diverse but taxonomically structured communities of microorganisms, the plant microbiota, that colonize every accessible plant tissue. Plant- associated microbiomes confer fitness advantages to the plant host, including growth promotion, nutrient uptake, stress tolerance and resistance to pathogens. In this Review, we explore how plant microbiome research has unravelled the complex network of genetic, biochemical, physical and metabolic interactions among the plant, the associated microbial communities and the environment. We also discuss how those interactions shape the assembly of plant- associated microbiomes and modulate their beneficial traits, such as nutrient acquisition and plant health, in addition to highlighting knowledge gaps and future directions.

Beneficial effects of the plant-associated microbiome. The plant- associated microbiome can provide benefits to the plant through various direct or indirect mechanisms. These benefits include growth promotion (blue), stress control (green) and defence against pathogens and pests (red). Microbiome- mediated benefits can be initiated in any part of a plant (mostly belowground) and can be transmitted to other parts via plant- mediated transport or signals (shown as blue, green and red dashed arrows, representing mechanisms that contribute to plant growth, stress relief and defence, respectively). Direct effects are mediated through nitrogen fixation, through unlocking of essential nutrients from minerals and through enhancing the capability of plants to take up nutrients from the soil. In addition, other direct effects include the stimulation of plant growth via stress alleviation, through the modulation of aminocyclopropane-1- carboxylate (ACC) deaminase expression and the production of plant hormones, detoxification enzymes and osmoprotectants. Benefits can also be indirect, as the plant- associated microbiome protects the plant against pathogens or pests through antagonism or through inducing systemic resistance in plants. Complex microorganism–microorganism and host–microorganism interactions maintain the balance between different members of the microbial community in favour of beneficial microorganisms that contribute to plant health (yellow). Diazotrophic bacteria can fix atmospheric nitrogen (N 2 ) and might actively transport ammonium (NH 4 + ) and nitrate (NO 3 − ) to the host. Ammonifying bacteria convert organic N 2 present in the soil to NH 4 + , which is further converted to NO 3 − by nitrifying bacteria. Leguminous plants develop root nodule symbiosis with N 2 - fixing bacteria. Arbuscular mycorrhizal fungi convert arginine (Arg) to urea and then to NH 4 + . Microbiomes can unlock essential elements by oxidizing, solubilizing or chelating minerals into plant- available nutrients such as phosphate (Pi), nitrogen (NH 4 + ) and potassium (K + ) through the production of organic acids and siderophores. Furthermore, arbuscular mycorrhizal fungi might enhance nutrient availability by long- distance transport through the mycelium and specialized structures called arbuscules (fungal hyphae ensheathed in a modified form of the cortical cell plasma membrane) that transport elements directly to the host cytoplasm. Microbiomes can stimulate plant growth by metabolizing tryptophan and other small molecules in the plant exudates and producing phytohormones that include auxins, gibberellins, cytokinins and phytohormone mimics. Auxins can also induce transcription of the ACC synthase that catalyses the formation of ACC. ACC, the direct precursor of ethylene, is metabolized by bacteria via the enzyme ACC deaminase, thus ameliorating abiotic stress. Members of plant- associated microbiomes produce a range of enzymes that can detoxify reactive oxygen species, thus minimizing plant- induced stress. The plant- associated microbiome protects the plant against pathogens by the production of antibiotics, lytic enzymes, volatiles and siderophores. Various microbial structures — such as secretion systems, flagella and pili — along with proteins such as effector proteins, indirectly contribute to plant defence by triggering an induced systemic resistance response. Siderophore- mediated nutrient competition between commensals and plant pathogens can reduce pathogen titres. Interkingdom and intrakingdom interactions within the microbiome maintain the microbial balance, thus protecting plants from dysbiosis. Furthermore, hub microorganisms can amplify host signals in order to promote the assembly of a microbiome that provides benefits to the plant. Overall, beneficial plant–microbiome interactions improve the growth performance and/or health of plants

https://go.nature.com/3fXCHBX
.

Beyond the Pale: The Earliest Agrarian States and “their Barbarians” 
Prof James C. Scott

Para estudiantes de biología de la Universidad Central de Venezuela:  

Fundamentos Teóricos del Manejo Ecológico de Plagas y Enfermedades

https://bit.ly/31R7T0J

A Mathematical Theory of Holobiont Evolution
Roughgarden 2020

This paper develops a mathematical theory for holobiont evolution that parallels the population-genetic theory of classical evolutionary biology. It presents theory for hologenomes having two haploid microbial strains and two diploid host alleles. The theory shows how selection on holobionts causes the joint evolution of microbial and host components of the hologenome. The theory also reveals the distribution of microbiome configurations across hosts as well as stable strategies for microbiome-host coadaptation.

Holobiont life cycle for holobiont whose microbiome consists of one or two microbial strains (green and/or brown circle) and whose nucleus consists of one allele (green or brown cog). In each generation the microbiomes for the juvenile hosts are assembled through binomial sampling from the microbial source pool. The host nuclear alleles are transmitted vertically from parent to juvenile with random union of gametes. At the holobiont selection stage, the diagram’s columns indicate the strains being contributed to the microbial source pool and the diagram’s rows indicate alleles being contributed to the host source pool. The microbial source pool is dilute—hologenotypes are assembled via binomial sampling of microbial strains. Generation time of microbes is short relative to host—microbiome comes to community equilibrium within each host generation. The figure illustrates how the transmission of host nuclear genes and the microbiome operate in parallel. The release of microbes to the microbe pool and the release of gametes to the gamete pool both enable genetic recombination in their respective components of the hologenome. Similarly, the statistical process of microbe colonization is the counterpart of the mating system for determining the pattern of inheritance for their respective components of the hologenome.

Trajectories of the combined dynamics of microbe frequency and allele frequency under holobiont selection leading to a combined polymorphism representing coadaptation between the microbiome and host. Trajectories all begin at various spots near the axes and converge through time to the green dot in the interior. The equilibrium frequencies are marked with the vertical and horizontal lines in green.

https://www.biorxiv.org/content/10.1101/2020.04.10.036350v1
.

An ecological framework for understanding the roles of Epichloë endophytes on plant defenses against fungal diseases 
Pérez et al., 2020

Epichloë fungal endophytes protect host plants against fungal pathogens.

This protection against pathogens can be either direct or indirect.

Endophytes reduce pathogen incidence and severity in host plant populations.

In seeds, the association with endophytes reduced pathogen colonization and infection.

Endophyte protection seems to be clear on debilitator and killer pathogens but not on castrators.

Plants harbor a wide diversity of microorganisms in their tissues. Some of them have a long co-evolutionary history with their hosts, likely playing a pivotal role in regulating the plant interaction with other microbes such as pathogens. Some cool-season grasses are symbiotic with Epichloë fungal endophytes that grow symptomless and systemically in aboveground tissues. Among the many benefits that have been ascribed to endophytes, their role in mediating plant interactions with pathogens has been scarcely developed. Here, we explored the effects of Epichloë fungal endophytes on the interaction of host grasses with fungal pathogens. We made a meta-analysis that covered a total of 18 host grass species, 11 fungal endophyte species, and 22 fungal pathogen species. We observed endophyte-mediated negative effects on pathogens in vitro and in planta. Endophyte negative effects on pathogens were apparent not only in laboratory but also in greenhouse and field experiments. Epichloë fungal endophytes had negative effects on pathogen growth and spores' germination. On living plants, endophytes reduced both severity and incidence of the disease as well as colonization and subsequent infection of seeds. Symbiosis with endophytes showed an inhibitory effect on debilitator and killer pathogens, but not on castrators, and this effect did not differ among biotrophic or necrotrophic lifestyles. We found that this protection can be direct through the production of fungistatic compounds, the competition for a common resource, or the induction of plant defenses, and indirect associated with endophyte-generated changes in the abiotic or the biotic environment. Several mechanisms operate simultaneously and contribute differentially to the reduction of disease within grass populations.

https://www.sciencedirect.com/science/article/abs/pii/S1749461320300233?via%3Dihub 

.

Spring and All [By the road to the contagious hospital] 

William Carlos Williams 

I

By the road to the contagious hospital
under the surge of the blue
mottled clouds driven from the
northeast-a cold wind. Beyond, the
waste of broad, muddy fields
brown with dried weeds, standing and fallen

patches of standing water
the scattering of tall trees

All along the road the reddish
purplish, forked, upstanding, twiggy
stuff of bushes and small trees
with dead, brown leaves under them
leafless vines—

Lifeless in appearance, sluggish
dazed spring approaches—

They enter the new world naked,
cold, uncertain of all
save that they enter. All about them
the cold, familiar wind—

Now the grass, tomorrow
the stiff curl of wildcarrot leaf
One by one objects are defined—
It quickens: clarity, outline of leaf

But now the stark dignity of
entrance—Still, the profound change
has come upon them: rooted, they
grip down and begin to awaken

Zoonotic host diversity increases in human-dominated ecosystems      
Gibb et al., 2020

Land use change—for example, the conversion of natural habitats to agricultural or urban ecosystems—is widely recognized to influence the risk and emergence of zoonotic disease in humans. However, whether such changes in risk are underpinned by predictable ecological changes remains unclear. It has been suggested that habitat disturbance might cause predictable changes in the local diversity and taxonomic composition of potential reservoir hosts, owing to systematic, trait-mediated differences in species resilience to human pressures. Here we analyse 6,801 ecological assemblages and 376 host species worldwide, controlling for research effort, and show that land use has global and systematic effects on local zoonotic host communities. Known wildlife hosts of human-shared pathogens and parasites overall comprise a greater proportion of local species richness (18–72% higher) and total abundance (21–144% higher) in sites under substantial human use (secondary, agricultural and urban ecosystems) compared with nearby undisturbed habitats. The magnitude of this effect varies taxonomically and is strongest for rodent, bat and passerine bird zoonotic host species, which may be one factor that underpins the global importance of these taxa as zoonotic reservoirs. We further show that mammal species that harbour more pathogens overall (either human-shared or non-human-shared) are more likely to occur in human-managed ecosystems, suggesting that these trends may be mediated by ecological or life-history traits that influence both host status and tolerance to human disturbance. Our results suggest that global changes in the mode and the intensity of land use are creating expanding hazardous interfaces between people, livestock and wildlife reservoirs of zoonotic disease.

https://www.nature.com/articles/s41586-020-2562-8

.

Confronting Complexity in Agroecology: Simple Models From Turing to Simon 

John Vandermeer, 2020

There are two interrelated issues that seem to be emerging as central to the understanding of ecological systems more generally, particularly relevant to agroecosystems. First is the key insights of Alan Turing in which spatial pattern emerges from a system in which there is a reaction between two objects, both of which are diffusing in space, a pest and its natural enemy, for example. Secondly, as small-scale farmers make complex decisions about their farm's ecosystem management, they are forced to contemplate market forces as much as the background ecology. This necessity automatically involves a time lag in that remuneration for produce is realized substantially after the decision to plant is made. Here, behavioral economics intersects with non-linear ecological dynamics to produce an expectation of chaotic patterns. It is suggested that these two core ideas, spatial dynamics (e.g., Turing's dynamic instability in space) and chaos (e.g., Simon's constrained rationality in farm decisions) form a qualitative theoretical foundation for understanding the ecology of agroecosystems.

From the locust plagues with which Yaweh threatened Egypt to the coffee rust disease that threatens the supply of the world's most important drug, the idea of an agricultural pest gives rise to the idea of control, the holy grail of Western civilization—control of nature, that is. I often wondered why Yaweh caused the Red Sea to part so as to provide the Israelites passage, when he could just as easily have sent a big boat for them, given his previous experience with gigantic boats. But the truth is that parting of the seas represents much more of a symbol, the control of nature, whereas a boat would have implied the rather unimpressive “working with nature.” Floating on water is far less impressive than making it behave miraculously. It was not really just about saving the Israelites, it was as much an attempt to prove dominance over nature.

Not all the world was as credulous as the forebears of the Judeo/Christian/Islamic tradition. Original people of the Guatemalan highlands apparently had no need for such a deity to solve their pest problems—they had no pests. When Helda Morales asked them what pests they had in their agricultural system, they all claimed to have no pests, yet when questioned about what “insects” they had in their system, they listed a host of species, many of which were known to Western science as “pests.” When asked why these insects were not pests, as the international experts claimed, these peasant farmers explained that they manage their farms so as “not to attract pests in the first place” (Morales and Perfecto, 2000).

Now known as the “Morales effect,” many traditional farming systems take this point of view. Structure the agroecosystem partly with the idea of not giving home or sustenance to organisms known to generate problems. If some insects or bacteria or viruses are known to be enemies of the plants or animals you are trying to culture, find a way of culturing such that these potential pests are “managed” in such a way that they never turn their actual status of “potential pests” into the actual status of “pest.”

As Albert Howard and Gabriella Mathais discovered when they went to India to “teach” the farmers the “modern ways” of agriculture that the empire had developed (Vandermeer and Perfecto, 2017), they saw the Morales effect operating in many ways, especially with regard to nutrient cycling, but more generally as a system that takes the natural systems of nature as givens, then prods and pokes them, using the understanding of the underlying operation of the ecosystem, to plan their farm. It is worth noting that the Howard/Mathais team was gaining its insights about ecology in the late nineteenth century, only a few decades after the word itself was coined by Haeckel (1870), and well before ecology became known as a scientific discipline. Their insights are even more remarkable given the virtual absence of background knowledge from formal science. Traditional knowledge is sometimes that way.

Now, after two centuries of very smart people doing very intelligent research in the field of ecology, we can say that the scientific background we have to work with is magnitudes more sophisticated than the tools that Howard and Mathais had to work with. Today we can combine traditional understanding of food provisioning with the partial understanding we have from formal science to produce what Richard Levins referred to as a gentle, thought intensive form of environmental management.

https://www.frontiersin.org/articles/10.3389/fsufs.2020.00095/full

.