Patricia Velez

Microfungal oasis in an oligotrophic desert: diversity patterns and community structure in three freshwater systems of Cuatro Ciénegas, Mexico

The Cuatro Ciénegas Basin (CCB) comprises several oligotrophic aquatic ecosystems limited by phosphorus. These aquatic systems are dominated by a high prokaryotic diversity, shaped by the stress of low nutrient supplies and interspecific competition. Although fungi constitute a diverse and important component of microbial diversity, the microfungal diversity in the CCB remains to be unveiled. With the aim to explore microfungal diversity and ecological patterns in this area, we present the first investigation analyzing cultivable taxa from sediment and water, as well as lignocellulolytic taxa obtained from incubated submerged plant debris, and wood panels in three contrasting freshwater systems in the CCB: Churince, Becerra and Pozas Rojas. We chose a culture-based approach to analyze sediment and water samples in order to obtain fungal cultures, providing opportunities for a posteriori studies, and the possibility of ex situ preservation of the diversity. We evaluated sequence data from the nuclear ribosomal internal transcribed spacer including the 5.8 rDNA region for 126 isolates, revealing 37 OTUs. These OTUs were phylogenetically affiliated to several genera in the fungal phyla: Zygomycota, Basidiomycota, and Ascomycota. We recorded two OTUs with saline affinity, agreeing with previous findings on the prokaryotic communities with ancestral marine resemblances. All the studied systems showed moderate diversity levels, however discrepancies among the diversity indexes were observed, due to the occurrence of abundant taxa in the samples. Our results indicated that lignocellulolytic microfungal communities are dominated by transient fungal taxa, as resident species were not recorded perhaps as a result of the long-term strong competition with the highly adapted prokaryotic community. Moreover, the obtained microfungal taxa occurred mostly on the resident plant debris, rather than submerged wood panels, perhaps as a result of the high adaptation to specific environmental conditions. In conclusion, the CCB possess a moderate taxonomical diversity compared to other arid environments, probably as a result of high selective pressures. Nonetheless, due to high spatial and temporal heterogeneity, the functional fungal diversity was considerable as predicted by the intermediate disturbance hypothesis. Decisively, the assessment of microfungal diversity freshwater systems is relevant, since this ecological group of microorganisms represents an important indicator of trophic complexity and biotic interactions among microbial communities, having important implications for understanding eukaryotic survival at the oligotrophic limit for life.

Diversity of marine ascomycetes from the disturbed sandy beaches of Tabasco, Mexico

The coastline of Tabasco State in the Gulf of Mexico represents a highly deteriorated ecosystem, where densely populated human settlements and large offshore petroleum developments are negatively affecting the marine biodiversity. Previous work on marine ascomycetes reported that in the Gulf of Mexico the diversity of these fungi might be threatened by anthropogenic activities. Therefore we evaluated the diversity of marine ascomycetes in this area, and registered 19 taxa. Ceriosporopsis capillacea was recorded for the first time for Mexico. The highest diversity was obtained in the beach of Sanchez Magallanes, which receives a great quantity and diversity of organic remains originating from El Carmen/Machona mangrove forests via the Santa Ana mouth, benefiting the proliferation of marine fungi. The lowest diversity was documented in the beach of Paraiso, which is close to the delta of one of the most polluted rivers in Mexico and to off-shore oil extraction platforms. We found a significant correlation between the community composition and abundance, implying that the overall abundance is defined by the community structure, perhaps as a result of competition. Additionally, our results indicated that there is no relationship between the grain size and the biodiversity observed.

Comparative Transcriptome Analysis of the Cosmopolitan Marine Fungus Corollospora maritima Under Two Physiological Conditions.

Marine sandy beaches represent dynamic environments often subject to harsh conditions and climate fluctuations, where natural and anthropogenic inputs of freshwater from fluvial and pluvial sources alter salinity, which has been recognized as a key variable affecting the distribution of aquatic organisms and influencing critical physiological processes. The marine arenicolous fungus Corollospora maritima is a worldwide-distributed saprobe that has been reported to present tolerance to freshwater. Here, we present a transcriptome analysis that will provide the first insight of the genomic content for this fungus and a gene expression comparison between two different salinity conditions. We also identified genes that are candidates for being differentially expressed in response to environmental variations on salinity during the fungal growth. The de novo reconstruction of C. maritima transcriptome Illumina sequencing provided a total of 14,530 transcripts (16 megabases). The comparison between the two growth conditions rendered 103 genes specifically overexpressed in seawater, and 132 genes specifically up-regulated under freshwater. Using fungal isolates collected from different beaches, the specific environmental regulation of particular transcript differential expression was confirmed by RT-qPCR. To our knowledge, this is the first analysis that explores the marine fungus C. maritima molecular responses to overcome freshwater stress, and these data could shed light to understand the fungal adaptation and plasticity mechanisms to the marine habitat.

Experimental and molecular approximation to microbial niche: trophic interactions between oribatid mites and microfungi in an oligotrophic freshwater system

Mite-fungal interactions play a key role in structuring core ecosystem processes such as nutrient dynamics. Despite their ecological relevance, these cross-kingdom interactions remain poorly understood particularly in extreme environments. Herein, we investigated feeding preferences of a novel genetic lineage of aquatic oribatids obtained from an oligotrophic freshwater system in the Cuatro Ciénegas Basin (CCB) within the Chihuahuan Desert, Mexico. During in vitro diet preference bioassays, transient aquatic microfungi (Aspergillus niger, Talaromyces sp., and Pleosporales sp.) recovered from the same mesocosm samples were offered individually and simultaneously to mites. Gut content was analyzed using classic plating and culture-independent direct PCR (focusing on the fungal barcoding region) methods. Our results indicated that oribatids fed on all tested fungal isolates, yet the profusely developing A. niger was preferentially consumed with all fungal components being digested. This feeding habit is particularly interesting since A. niger has been reported as an unsuitable dietary element for population growth, being consistently avoided by mites in previous laboratory experiments. It is possible that our mites from the CCB have adapted to exploit available resources within this oligotrophic site. This work confirms the trophic relationship between microfungi and mites, two rarely investigated major components of the microbial community, shedding light on the niche dynamics under low-nutrient conditions.

Nutrient Dependent Cross-Kingdom Interactions: Fungi and Bacteria From an Oligotrophic Desert Oasis

Microbial interactions play a key role in ecosystem functioning, with nutrient availability as an important determinant. Although phylogenetically distant bacteria and fungi commonly co-occur in nature, information on their cross-kingdom interactions under unstable, extreme environments remains poor. Hence, the aims of this work were to evaluate potential in vitro interactions among fungi and bacteria isolated from a phosphorous oligotrophic aquatic system in the Cuatro Ciénegas Basin, Mexico, and to test the nutrients-based shifts. We assessed growth changes in bacteria (Aeromonas and Vibrio) and fungi (Coprinellus micaceus, Cladosporium sp., and Aspergillus niger) on co-cultures in relation to monocultures under diverse nutrient scenarios on Petri dishes. Interactions were explored using a network analysis, and a metabolome profiling for specific taxa. We identified nutrient-dependent patterns, as beneficial interactions dominated in low-nutrients media and antagonistic interactions dominated in rich media. This suggests that cross-kingdom synergistic interactions might favor microbial colonization and growth under low nutrient conditions, representing an adaptive trait to oligotrophic environments. Moreover, our findings agree with the stress-gradient hypothesis, since microbial interactions shifted from competition to cooperation as environmental stress (expressed as low nutrients) increased. At a functional level consistent differences were detected in the production of secondary metabolites, agreeing with plate bioassays. Our results based on culture experiments, provides evidence to understand the complexity of microbial dynamics and survival in phosphorous-depleted environments.

The Niche at the Edge of Life or the Microbial Ecology (Including Microfungi) of Cuatro Ciénegas: Mutualisms with Locals, Antagonisms Against Foreigners

In this chapter we will explore whether the niche concept is useful to understand microbes, since we believe that this key concept in ecology is particularly useful in the investigation of microbial biodiversity. On the one hand, with microbes we can conduct experiments to analyze in detail all the aspects of the Grinnellian niche, in a way that cannot be done in other organisms. On the other hand, even if complicated, we can develop different experiments and observations to start analyzing the Eltonian aspects of the niche. Here we develop our ideas on how to study the niche components in microbial systems and describe our advances in analyzing these components in a particular group of organisms in the Cuatro Cienegas Basin (CCB). In this oasis, the distinctive oligotrophic conditions of several freshwater systems in CCB promote unique microbial interactions in order to cope with nutrient stress, where antagonist and synergic effects influence bacterial diversity structure, modifying the nature and intensity of biotic interactions. For example, Bacillus has few antagonistic interactions among strains of a given sampling site but strong antagonisms when competing against strains from different sites. Interestingly, antagonistic strains belonged to two genetically close species, and their targets belonged to taxonomically separate groups. Even more so, the same Bacillus strains showed great diversity in the dependence of the different strains on other community members. While antagonistic strains were in general prototrophs, a large proportion of sensitive and resistant strains exhibited auxotrophy suggesting that they need their community in order to survive. At CCB we believe that the cohesion of the community through these positive interactions is paramount to explain survival in such a harsh environment. As a result, the multidimensional space where the theater of life plays in CCB is very rich and full of actors, which shifts constantly, as virus and other process “chop the head” of the dominant species and former “underdogs” of the rare biosphere take their roles. Finally, since this play of “life at the edge” has been continued in the same site for a very long time with coevolving communities, here the “conversations and negotiations” between microscopic actors seem to be the reason why this stage has persisted for such a long time.

The Effect of Nutrient Availability on the Ecological Role of Filamentous Microfungi: Lessons from Elemental Stoichiometry

Ecological stoichiometry theory helps us to better understand trophic interactions by analyzing the imbalances in the relative supplies of key elements (carbon, nitrogen, and phosphorus) between organisms and their resources. However, the mechanisms that control elemental stoichiometry in different taxonomic groups and the effects of nutrient supply imbalances are not yet clear. Aquatic microfungi are an ecological group of microorganisms ranging from those adapted to complete their life cycles in aquatic habitats to those that occurring in water fortuitously. Aquatic fungi are important regulators of plant productivity, community dynamics, and diversity in nutrient-poor and extreme ecosystems. Because aquatic fungi are heterotrophs, it has been assumed that they possess high degree of stoichiometric homeostasis. However, data concerning their elemental composition and their degree of homeostasis remain scarce. Herein, we analyzed the C:N:P stoichiometry of mycelia in ten aquatic microfungi isolated from three hydrological systems with different nutrient conditions within Cuatro Cienegas Basin (CCB). Our hypotheses were (a) variations in C:N:P ratios reflect divergent life history strategies between the three environments, independently of the fungal taxa involved, and (b) C:N:P ratios reflect physiological adjustments associated with specific taxa, independent of the environmental characteristics. Our results provide some support for the first hypothesis, as the apparent capacity for elemental stoichiometry regulation in the aquatic microfungi was not linked to phylogenetic relationships but appeared to be an adaptation to resource availabilities in the environment in which they grew. The microfungi isolated from the most oligotrophic site within the CCB (Pozas Rojas) most strongly regulated their elemental stoichiometry in comparison with fungal isolates from other sites within CCB.

Genetic diversity and population structure of Corollospora maritima sensu lato: new insights from population genetics

Abstract The study of genetic variation in fungi has been poor since the development of the theoretical underpinnings of population genetics, specifically in marine taxa. Corollospora maritima sensu lato is an abundant cosmopolitan marine fungus, playing a crucial ecological role in the intertidal environment. We evaluated the extent and distribution of the genetic diversity in the nuclear ribosomal internal transcribed spacer region of 110 isolates of this ascomycete from 19 locations in the Gulf of Mexico, Caribbean Sea and Pacific Ocean. The diversity estimates demonstrated that C. maritima sensu lato possesses a high genetic diversity compared to other cosmopolitan fungi, with the highest levels of variability in the Caribbean Sea. Globally, we registered 28 haplotypes, out of which 11 were specific to the Caribbean Sea, implying these populations are genetically unique. We detected populations inhabiting human-impacted sites with null genetic variation. As long-term exposure to contaminants has been proven to decrease genetic diversity, a conservation genetics approach to assess this matter is urgent. Our results revealed the occurrence of five genetic lineages with distinctive environmental preferences and an overlapping geographical distribution, agreeing with previous studies reporting physiological races within this species.