Plants and their arbuscular mycorrhizal fungal symbionts interact in complex underground networks involving multiple partners. This increases the potential for exploitation and defection by individuals, raising the question of how partners maintain a fair, two-way transfer of resources. We manipulated cooperation in plants and fungal partners to show that plants can detect, discriminate, and reward the best fungal partners with more carbohydrates. In turn, their fungal partners enforce cooperation by increasing nutrient transfer only to those roots providing more carbohydrates. On the basis of these observations we conclude that, unlike many other mutualisms, the symbiont cannot be "enslaved." Rather, the mutualism is evolutionarily stable because control is bidirectional, and partners offering the best rate of exchange are rewarded.

https://science.sciencemag.org/content/sci/333/6044/880.full.pdf

Reciprocal Rewards Stabilize Cooperation in the Mycorrhizal Symbiosis

https://www.cell.com/trends/microbiology/pdf/S0966-842X(10)00215-5.pdf

Nitrogen fixation by marine cyanobacteria

Summary • At present, molecular ecological studies of arbuscular mycorrhizal fungi (AMF) are only possible above species level when targeting entire communities. To improve molecular species characterization and to allow species level community analyses in the field, a set of newly designed AMF specific PCR primers was successfully tested.  Nuclear rDNA fragments from diverse phylogenetic AMF lineages were sequenced and analysed to design four primer mixtures, each targeting one binding site in the small subunit (SSU) or large subunit (LSU) rDNA. To allow species resolution, they span a fragment covering the partial SSU, whole internal transcribed spacer (ITS) rDNA region and partial LSU.  The new primers are suitable for specifically amplifying AMF rDNA from material that may be contaminated by other organisms (e.g., samples from pot cultures or the field), characterizing the diversity of AMF species from field samples, and amplifying a SSU-ITS-LSU fragment that allows phylogenetic analyses with species level resolution.  The PCR primers can be used to monitor entire AMF field communities, based on a single rDNA marker region. Their application will improve the base for deep sequencing approaches; moreover, they can be efficiently used as DNA barcoding primers.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2009.02835.x

DNA-based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi.

The biodiversity of arbuscular mycorrhizal fungi (AMF) communities present in five Sardinian soils (Italy) subjected to different land-use (tilled vineyard, covered vineyard, pasture, managed meadow and cork-oak formation) was analysed using a pyrosequencing-based approach for the first time. Two regions of the 18S ribosomal RNA gene were considered as molecular target. The pyrosequencing produced a total of 10924 sequences: 6799 from the first and 4125 from the second target region. Among these sequences, 3189 and 1003 were selected to generate operational taxonomic units (OTUs) and to evaluate the AMF community richness and similarity: 117 (37 of which were singletons) and 28 (nine of which were singletons) unique AMF OTUs were detected respectively. Within the Glomeromycota OTUs, those belonging to the Glomerales order were dominant in all the soils. Diversisporales OTUs were always detected, even though less frequently, while Archaeosporales and Paraglomerales OTUs were exclusive of the pasture soil. Eleven OTUs were shared by all the soils, but each of the five AMF communities showed particular features, suggesting a meaningful dissimilarity among the Glomeromycota populations. The environments with low inputs (pasture and covered vineyard) showed a higher AMF biodiversity than those subjected to human input (managed meadow and tilled vineyard). A reduction in AMF was found in the cork-oak formation because other mycorrhizal fungal species, more likely associated to trees and shrubs, were detected. These findings reinforce the view that AMF biodiversity is influenced by both human input and ecological traits, illustrating a gradient of AMF communities which mirror the land-use gradient. The high number of sequences obtained by the pyrosequencing strategy has provided detailed information on the soil AMF assemblages, thus offering a source of light to shine on this crucial soil microbial group.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1462-2920.2009.02099.x

Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach.

Climate change will alter concurrently many environmental factors that exert control over oceanic phytoplankton. Recent laboratory culture work, shipboard experiments, and field surveys reveal many remaining unknowns about the bottom-up controls for five globally important algal groups. Increasing uncertainties exist, respectively, for picocyanobacteria, diatoms, Phaeocystis spp., N2-fixing cyanobacteria, and coccolithophores. This missing information about current environmental controls will hinder progress in modeling how these phytoplankton will be influenced by climate change. A review of conceptual approaches used to elucidate the relationship between environmental controls and phytoplankton dominance, from Margalef's mandala to functional traits, uncovered limitations regarding their application to climate-change scenarios. For example, these previous approaches have insufficient scope or dimensions to take into account the confounding effects of synergistic and antagonistic interactions of multiple environmental change variables. A new approach is needed that considers all of the different environmental properties altered by climate change and their interactions while at the same time permitting a subset of the most significant controls for a specific phytoplankton group to be isolated and evaluated in factorial matrix perturbation experiments. We advocate three new interlinked approaches, including environmental clusters that incorporate all factors (temperature, CO2, light, nutrients, and trace metals), which both exert control over present-day floristics and will be altered by climate change. By carefully linking a holistic conceptual approach to a reductionist experimental design, the future responses of open-ocean phytoplankton groups to a complex, rapidly changing environment can be better predicted.

/pdf/environmental-control-of-open-ocean-phytoplankton-groups-now-4c1m5x7q9p.pdf

Environmental control of open-ocean phytoplankton groups: Now and in the future

To understand the structure of marine diazotrophic communities in the tropical and subtropical Atlantic Ocean, the molecular diversity of the nifH gene was studied by nested PCR amplification using degenerate primers, followed by cloning and sequencing. Sequences of nifH genes were amplified from environmental DNA samples collected during three cruises (November-December 2000, March 2002, and October-November 2002) covering an area between 0 to 28.3°N and 56.6 to 18.5°W. A total of 170 unique sequences were recovered from 18 stations and 23 depths. Samples from the November-December 2000 cruise contained both unicellular and filamentous cyanobacterial nifH phylotypes, as well as γ-proteobacterial and cluster III sequences, so far only reported in the Pacific Ocean. In contrast, samples from the March 2002 cruise contained only phylotypes related to the uncultured group A unicellular cyanobacteria. The October-November 2002 cruise contained both filamentous and unicellular cyanobacterial and γ-proteobacterial sequences. Several sequences were identical at the nucleotide level to previously described environmental sequences from the Pacific Ocean, including group A sequences. The data suggest a community shift from filamentous cyanobacteria in surface waters to unicellular cyanobacteria and/or heterotrophic bacteria in deeper waters. With one exception, filamentous cyanobacterial nifH sequences were present within temperatures ranging between 26.5 and 30°C and where nitrate was undetectable. In contrast, nonfilamentous nifH sequences were found throughout a broader temperature range, 15 to 30°C, more often in waters with temperature of <26°C, and were sometimes recovered from waters with detectable nitrate concentrations.

Diazotrophic diversity and distribution in the tropical and subtropical Atlantic Ocean.

Summary
• Glomus intraradices is a widespread arbuscular mycorrhizal fungus (AMF), which has been found in an extremely broad range of habitats, indicating a high tolerance for environmental factors and a generalist life history strategy. Despite this ecological versatility, not much is known about the genetic diversity of this fungal species across different habitats or over large geographic scales.
• A nested polymerase chain reaction (PCR) approach for the mitochondrial rRNA large subunit gene (mtLSU), distinguished different haplotypes among cultivated isolates of G. intraradices and within mycorrhizal root samples from the field.
• From analysis of 16 isolates of this species originating from five continents, 12 mitochondrial haplotypes were distinguished. Five additional mtLSU haplotypes were detected in field-collected mycorrhizal roots. Some introns in the mtLSU region appear to be stable over years of cultivation and are ancestral to the G. intraradices clade.
• Genetic diversity within G. intraradices is substantially higher than previously thought, although some mtLSU haplotypes are widespread. A restriction fragment length polymorphism approach also was developed to distinguish mtLSU haplotypes without sequencing. Using this molecular tool, intraspecific genetic variation of an AMF species can be studied directly in field plants.

Genetic diversity of the arbuscular mycorrhizal fungus Glomus intraradices as determined by mitochondrial large subunit rRNA gene sequences is considerably higher than previously expected

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Diazotrophic diversity and distribution in the tropical and subtropical Atlantic Ocean.

Genetic diversity of the arbuscular mycorrhizal fungus Glomus intraradices as determined by mitochondrial large subunit rRNA gene sequences is considerably higher than previously expected