Chlorophyll a

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En la naturaleza salvaje pierdo todo sentido de los límites 

J.M. Coetzee
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Cascading regime shifts within and across scales
Rocha et al.

Regime shifts are large, abrupt and persistent critical transitions in the function and structure of systems. Yet it is largely unknown how these transitions will interact, whether the occurrence of one will increase the likelihood of another, or simply correlate at distant places. Here we explore two types of cascading effects: domino effects create one-way dependencies, while hidden feedbacks produce two-way interactions; and compare them with the control case of driver sharing which can induce correlations. Using 30 regime shifts described as networks, we show that 45% of the pair-wise combinations of regime shifts present at least one plausible structural interdependence. Driver sharing is more common in aquatic systems, while hidden feedbacks are more commonly found in terrestrial and Earth systems tipping points. The likelihood of cascading effects depends on cross-scale interactions, but differs for each cascading effect type. Regime shifts should not be studied in isolation: instead, methods and data collection should account for potential teleconnections.

Minimal examples of the cascading effects. We merged pairs of regime shifts causal networks and created a response variable matrix that accounted for drivers shared, domino effects, or hidden feedbacks for all pair-wise combinations of regime shifts. For example, for drivers sharing two minimal regime shifts are depicted as causal diagrams, drivers are coloured red and variables inside feedbacks purple. The joint network is represented as a 2-mode network which allows us to study the co-occurrence of drivers across regime shifts. The response variable matrix counts the drivers shared by all pair-wise combinations of regime shifts. In the example of a domino effect two regime shifts are joined together where driver c in regime shift 2 is part of a feedback process in regime shift 1, creating a one-way dependency (orange colored link) between the two regime shifts. The response variable matrix counts all the one-way causal pathways between pair-wise combinations of regime shifts. In the example of a hidden feedback, two minimal regime shifts when joined together give rise to a new unidentified feedback of length 4 (orange circular pathway). The response variable matrix counts all hidden feedbacks that arise when merging all pair-wise combinations of regime shifts. Labelled matrices of the resulting response variables are available in the supplementary material.

Driver sharing. The distribution of drivers shared per regime shift (a) with respect to the number of drivers each one has (black points) shows that regime shifts in aquatic environments tend to have and share more drivers. (b) shows the drivers most shared. WAIS abbreviates West Antarctica Ice Sheet collapse.

https://www.biorxiv.org/content/10.1101/364620v1

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Highland cattle (Scottish Gaelic: Bò Ghàidhealach; Scots: Heilan coo)

Global population density maps for cattle, buffaloes, sheep, goats, horses, pigs, chickens and ducks

 

https://buff.ly/2u5BFOU

Microbial interkingdom interactions in roots promote arabidopsis survival

Durán et al., 2019

Plant roots are associated with highly structured microbial communities composed of bacteria, fungi, and oomycetes. How these microbes interact to influence plant health has remained poorly studied. Although it is generally believed that a balanced soil microbial community is critical, how different components of the community influence each other and how they influence plant health are unknown. The study led by Schulze-Lefert and Stéphane Hacquard investigated microbial community structures of three natural populations of Arabidopsis from different geographical locations. They conducted profiling analyses of relative abundance and operational taxonomic units (OTUs) of root-associated bacteria, fungi, and oomycetes, and investigated intra- and inter-kingdom relationships of the communities. These uncovered a striking difference between inter-kingdom and intra-kingdom interactions. While the bacterial-fungal interactions were predominantly negative, the bacterial and fungal intra-kingdom interactions were predominantly positive.

To experimentally determine how the bacterial community interacts with fungal and oomycetal communities, the authors established culture collections covering significant proportions of the observed OTUs of bacteria, fungi, and oomycetes. They then adopted a gnotobiotic system to reconstitute microbial communities, so that they can determine impact of different communities on plant health and influence between different communities. Strikingly, they found that inoculation of sterile soil with a fungal or oomycetal community in the absence of bacteria led to low to zero survival rates of plants, indicating detrimental effects of fungal and oomycetal communities on plant health. In contrast, the addition of bacterial community provided not only positive growth benefits to Arabidopsis plants, but also full protection against fungi and oomycetes. As a large proportion of these fungi and oomycetes are plant pathogens, the results indicate that the plant immune system is unable to defend against these pathogens and that the root-associated bacterial community plays a decisive role in protecting plants from these pathogens. Consistent with observations from natural communities, the synthetic bacterial community had a large negative effect on fungal and oomycetal communities.

Pair-wise interaction analyses of individual bacterial strains on fungal growth showed that Comamonadaceae and Pseudomonadaceae had greatest antagonistic effects against diverse fungal isolates. Depletion of these two groups of bacteria from the synthetic community resulted in reduced protection against fungi. However, this Comamonadaceae- and Pseudomonadaceae-depleted bacterial community still provided profound protection against the fungal community in the gnotobiotic system, indicating that plant health protection against fungal pathogens is a highly redundant function in commensal bacteria. Together, this study advances our understanding of inter-kingdom interactions in root-associated microbial communities and provides much needed insights into the role of microbial community in plant health. The successful application of a gnotobiotic system and synthetic communities opens up new horizons for plant immunity studies and development of better biocontrol agents. 

https://bit.ly/2FaDX7G 

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Corn Face

Vascular bundle of a Zea mays (corn) stem as seen through the microscope. The 'eyes' and 'nose' of the face are large vessels that transport water and minerals to the leaves.

Photo:  Olivier Leroux

Interactive map to explore links between where food crops come from, their native origins, traditional regions of diversity and where they are now eaten worldwide

 https://tinyurl.com/y4qa5tv8

Map showing the rapid spread of potato late-blight in the 1840s 

In just 3 months, this crop disease spread from Belgium down to Spain, across to Ireland and up to Norway (all in an age before motorized transport)

@2blades
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The Cactaceae: descriptions and illustrations of plants of the cactus family.
By  Britton, Nathaniel Lord (1859-1934)
https://bit.ly/2F4shBc
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Lily pollen under the microscope! 
63x (objective lens magnification) Confocal 
Photo: Dr. David A. Johnston

Worldwide decline of the entomofauna: A review of its drivers 
FranciscoSánchez-Bayoa,  Kris A.G.Wyckhuys

Highlights  
•      Over 40% of insect species are threatened with extinction.
•      Lepidoptera, Hymenoptera and dung beetles (Coleoptera) are the taxa most affected.
•      Four aquatic taxa are imperiled and have already lost a large proportion of species. 
•      Habitat loss by conversion to intensive agriculture is the main driver of the declines. 
•      Agro-chemical pollutants, invasive species and climate change are additional causes.  

Abstract  

Biodiversity of insects is threatened worldwide. Here, we present a comprehensive review of 73 historical reports of insect declines from across the globe, and systematically assess the underlying drivers. Our work reveals dramatic rates of decline that may lead to the extinction of 40% of the world's insect species over the next few decades. In terrestrial ecosystems, Lepidoptera, Hymenoptera and dung beetles (Coleoptera) appear to be the taxa most affected, whereas four major aquatic taxa (Odonata, Plecoptera, Trichoptera and Ephemeroptera) have already lost a considerable proportion of species. Affected insect groups not only include specialists that occupy particular ecological niches, but also many common and generalist species. Concurrently, the abundance of a small number of species is increasing; these are all adaptable, generalist species that are occupying the vacant niches left by the ones declining. Among aquatic insects, habitat and dietary generalists, and pollutant-tolerant species are replacing the large biodiversity losses experienced in waters within agricultural and urban settings. The main drivers of species declines appear to be in order of importance: i) habitat loss and conversion to intensive agriculture and urbanisation; ii) pollution, mainly that by synthetic pesticides and fertilisers; iii) biological factors, including pathogens and introduced species; and iv) climate change. The latter factor is particularly important in tropical regions, but only affects a minority of species in colder climes and mountain settings of temperate zones. A rethinking of current agricultural practices, in particular a serious reduction in pesticide usage and its substitution with more sustainable, ecologically-based practices, is urgently needed to slow or reverse current trends, allow the recovery of declining insect populations and safeguard the vital ecosystem services they provide. In addition, effective remediation technologies should be applied to clean polluted waters in both agricultural and urban environments.

Annual rate of decline of the three major taxa studied (percentage of species declining per year) and of insect biomass.

https://tinyurl.com/y6l4zxo8

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'Man O War' from Coral Morphologic on Vimeo.

Domesticación

Plant chemical mediation of ant behavior
Annika S Nelson, Nalleli Carvajal Acosta, Kailen A Mooney

Highlights  
•      Ants occupy many trophic levels and roles in association with plants. 
•      Plants produce volatile and non-volatile chemicals that mediate ant behavior. 
•      Ant responses to plant chemicals are both innate and learned and occur at the level of the individual and colony.  

Ants are ecologically dominant members of terrestrial communities. Ant foraging is often strongly associated with plants and depends upon associative learning of chemicals in the environment. As a result, plant chemicals can affect ant behaviors and, in so doing, have strong multi-trophic indirect effects. Plant chemicals mediate ant behaviors in the contexts of floral visitation, seed dispersal and predation, leaf cutting, interactions with ant-mutualist host plants, interactions with mutualist and prey insects in plant canopies, and plant predation of ants by carnivorous plants. Here, we review what is known about these differing contexts in which plant chemicals influence ant behavior, the mechanisms by which ants are affected by plant chemicals, and future directions within these topics.

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https://www.sciencedirect.com/science/article/pii/S2214574518301214
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If our small minds, for some convenience, divide this universe, into parts - physics, biology, geology, astronomy, psychology, and so on - remember that nature does not know it!

Richard Feynman ‏ 
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Organicfarming performs better across the sdgs in general, however, the global budget for research in organic is still less than 1% of all agricultural research.
 @IFOAMorganic

Trissolcus japonicus

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"The basic mode of ecological awareness is anxiety, the feeling that things have lost their seemingly original significance, the feeling that something creepy is happening, close to home" 

Timothy Morton - Dark Ecology 

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The state of our ecosystems...

Large-scale replicated field study of maize rhizosphere identifies heritable microbes 

William A. Walters et al. 2019.

Significance  

In this very large-scale longitudinal field study of the maize rhizosphere microbiome, we identify heritable taxa. These taxa display variance in their relative abundances that can be partially explained by genetic differences between the maize lines, above and beyond the strong influences of field, plant age, and weather on the diversity of the rhizosphere microbiome. If these heritable taxa are associated with beneficial traits, they may serve as phenotypes in future breeding endeavors

Abstract  

Soil microbes that colonize plant roots and are responsive to differences in plant genotype remain to be ascertained for agronomically important crops. From a very large-scale longitudinal field study of 27 maize inbred lines planted in three fields, with partial replication 5 y later, we identify root-associated microbiota exhibiting reproducible associations with plant genotype. Analysis of 4,866 samples identified 143 operational taxonomic units (OTUs) whose variation in relative abundances across the samples was significantly regulated by plant genotype, and included five of seven core OTUs present in all samples. Plant genetic effects were significant amid the large effects of plant age on the rhizosphere microbiome, regardless of the specific community of each field, and despite microbiome responses to climate events. Seasonal patterns showed that the plant root microbiome is locally seeded, changes with plant growth, and responds to weather events. However, against this background of variation, specific taxa responded to differences in host genotype. If shown to have beneficial functions, microbes may be considered candidate traits for selective breeding.

Environment and age strongly structure the rhizosphere microbial community. PCoA of unweighted (A and B) and weighted (C and D) UniFrac distances for maize rhizosphere and bulk soil samples. A and B show the same projection of the data, as do C and D. Symbols represent microbiomes and are colored by plant age (A and C; sampling week; see color gradient) by environment (B and D; by the specific field of origin). The first three PCs are plotted with the percentage of variation explained by each PC.

 Broad-sense heritability of individual OTUs for the 2010 field study. The broad-sense heritability (H²) is shown for the 100 OTUs with highest H² values. Circles show the actual H² values for each OTU in decreasing order and blue distributions show the corresponding H² values from 5,000 permutations of the data. Red circles indicate OTUs with P values ≤0.001. Taxonomies shown are most specific for each OTU.

Phylogeny of heritable OTUs. The tree shows the phylogenetic relationships of OTUs found in 80% of all rhizosphere samples. Heritable OTUs have branches colored in red. Major phyla are color-coded in the outer circle, and the deepest named taxonomy is given for each OTU. The tree is a subset of the Aug 2013 Greengenes tree. (Scale bar indicates inferred mutation rate per site.).

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https://www.pnas.org/content/115/28/7368

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Winter Trees (1963) S.R. Badmin
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