On Operational Taxonomic Units Research Articles

Integrated production of biopolymers with industrial wastewater treatment: Effects of OLR on process yields, biopolymers characteristics and mixed microbial community enrichment

The production of polyhydroxyalkanoates (PHA) using industrial wastewaters as feedstocks is a current and challenging topic. This study investigated the production of biopolymers by a mixed microbial culture under different OLRs equal to 1 kgCOD m−3d−1 (Period 1), 2 kgCOD m−3d−1 (Period 2) and 3 kgCOD m−3d−1 (Period 3). The maximum PHA content was achieved in Period 2 (0.38 gPHA gTSS−1), whereas lower values were obtained in Period 1 (0.13 gPHA gTSS−1) and Period 3 (0.26 gPHA gTSS−1). Overall, the maximum PHA productivity resulted equal to 0.08 gPHA L−1 h−1 (P2), 0.05 gPHA L−1 h−1 (P1) and 0.04 gPHA L−1 h−1 (P3), respectively.The molecular weight of the PHA increased from Period 1 (250 kDa) to Period 2 (417 KDa) and Period 3 (463 KDa), although resulting in a slight decrease of crystallinity degree. Microbial community analysis revealed a reduction in bacterial diversity and a progressive shift of the microbial community with the increasing OLR. Alpha-diversity indexes based on Operational Taxonomic Units (OTUs) at 99% identity revealed higher species richness (Taxa (S) 280) and diversity (Shannon (H) 4,06) in Period 1, whereas Period 3 was characterized by reduced richness and diversity and higher dominance (Taxa (S) 133, Shannon (H) 2,40).Based on the results obtained, it was pointed out that the OLR variation determined significant effects on the process performances, as well as on the productivity and quality of the biopolymers. This means that OLR is a key control parameter to maximize the PHA production and control the physical-chemical characteristics of the polymers.

Systemic lupus erythematosus patients have a distinct structural and functional skin microbiota compared with controls.

The skin is the second most affected organ after articular involvement in systemic lupus erythematosus (SLE) patients. Cutaneous involvement occurs in approximately 80% of patients during the course of SLE. Interaction between the host and skin microorganism is a complex process. There are few studies on the diversity of skin microbes in SLE patients. Therefore, this study aims to explore the relationship between skin microorganisms and SLE. A total of 20 SLE patients, 20 controls with rosacea and 20 healthy controls were selected as study subjects. Both the skin microbiota of rash region and non-rash region for each SLE patient were collected.16S rRNA gene sequencing was used to detected skin microbiota from 80 specimens. α-Diversity and β-diversity of skin microbiota were analyzed based on operational taxonomic units (OTUs) and minimal entropy decomposition (MED). Using Wilcoxon test and Linear Discriminate Analysis Effect Size (LEfSe), skin microbial diversity and composition were analyzed. Functional capabilities of microbiota were estimated through Kyoto Encyclopedia of Genes and Genomes database. Compared to rash region of SLE, diversity and richness were increased in healthy controls, and decreased in non-rash region of SLE and rash region of controls with rosacea. Additionally, changes of skin microbial composition were found at different taxonomic levels between four groups. For example, genus Halomonas was increased and genera Pelagibacterium, Novosphingobium, and Curvibacter were decreased in rash region compared to non-rash region of SLE based on OTUs and MED. Based on OTUs, metabolic pathways were also found differences in SLE patients, such as Xenobiotics Biodegradation and Metabolism. Compositions and diversity of skin microbiota in SLE patients are changed. This pilot study provides some suggestive evidence for further exploration of skin microbiota in SLE patients with cutaneous involvement.

Global AM fungi are dominating mycorrhizal communities in a tropical premontane dry forest in Laipuna, South Ecuador

Tropical dry forests are an intricate ecosystem with special adaptations to periods of drought. Arbuscular mycorrhizal fungi (AMF) are essential for plant survival in all terrestrial ecosystems but might be of even greater importance in dry forests as plant growth is limited due to nutrient and water deficiency during the dry season. Tropical dry forests in Ecuador are highly endangered, but studies about AMF communities are scarce. We investigated the AMF community of a premontane semi-deciduous dry forest in South Ecuador during the dry season. We estimated AMF diversity, distribution, and composition of the study site based on operational taxonomic units (OTUs) and compared the results to those from the tropical montane rainforest and páramo in South Ecuador. OTU delimitation was based on part of the small ribosomal subunit obtained by cloning and Sanger sequencing. Nearly all OTUs were Glomeraceae. The four frequent OTUs were Glomus, and comparison with the MaarjAM database revealed these to be globally distributed with a wide range of ecological adaptations. Several OTUs are shared with virtual taxa from dry forests in Africa. Ordination analysis of AMF communities from the tropical dry and montane rainforests in South Ecuador revealed a unique AMF community in the dry forest with only few overlapping OTUs. Most OTUs that were found in both dry and rainforests and on the two continents were globally distributed Glomus.

Analysis of Microbial Communities in Aged Refuse Based on 16S Sequencing

Aged refuse is widely considered to have certain soil fertility. 16S rRNA amplicon sequencing is used to investigate the microbial community of aged refuse. The aged refuse is found to contain higher soil fertility elements (total nitrogen, total phosphorus, total potassium, etc.) and higher concentrations of heavy metals (Pb, Cd, Zn, and Hg). Taxonomy based on operational taxonomic units (OTUs) shows that Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes are the main bacterial phyla in the two soils and there is a palpable difference in the microbial community composition between the two groups of samples. The genera Paramaledivibacter, Limnochorda, Marinobacter, Pseudaminobacter, Kocuria, Bdellovibrio, Halomonas, Gillisia, and Membranicola are enriched in the aged refuse. Functional predictive analysis shows that both the control soil and aged refuse have a high abundance of “carbohydrate metabolism” and “amino acid metabolism”, and show differences in the abundance of several metabolism pathways, such as “xenobiotics biodegradation and metabolism” and “lipid metabolism”. Aged refuse and undisturbed soil show significant differences in alpha diversity and microbial community composition. Multiple environmental factors (Hg, TN, Cr, Cd, etc.) significantly impact microorganisms’ abundance (Marinobacter, Halomonas, Blastococcus, etc.). Our study provides valuable knowledge for the ecological restoration of closed landfills.

Prebiotic effect of inulin-type fructans on faecal microbiota and short-chain fatty acids in type 2 diabetes: a randomised controlled trial

PurposeCompared to a healthy population, the gut microbiota in type 2 diabetes presents with several unfavourable features that may impair glucose regulation. The aim of this study was to evaluate the prebiotic effect of inulin-type fructans on the faecal microbiota and short-chain fatty acids (SCFA) in patients with type 2 diabetes.MethodsThe study was a placebo controlled crossover study, where 25 patients (15 men) aged 41–71 years consumed 16 g of inulin-type fructans (a mixture of oligofructose and inulin) and 16-g placebo (maltodextrin) for 6 weeks in randomised order. A 4-week washout separated the 6 weeks treatments. The faecal microbiota was analysed by high-throughput 16S rRNA amplicon sequencing and SCFA in faeces were analysed using vacuum distillation followed by gas chromatography.ResultsTreatment with inulin-type fructans induced moderate changes in the faecal microbiota composition (1.5%, p = 0.045). A bifidogenic effect was most prominent, with highest positive effect on operational taxonomic units (OTUs) of Bifidobacterium adolescentis, followed by OTUs of Bacteroides. Significantly higher faecal concentrations of total SCFA, acetic acid and propionic acid were detected after prebiotic consumption compared to placebo. The prebiotic fibre had no effects on the concentration of butyric acid or on the overall microbial diversity.ConclusionSix weeks supplementation with inulin-type fructans had a significant bifidogenic effect and induced increased concentrations of faecal SCFA, without changing faecal microbial diversity. Our findings suggest a moderate potential of inulin-type fructans to improve gut microbiota composition and to increase microbial fermentation in type 2 diabetes.Trial registrationThe trial is registered at clinicaltrials.gov (NCT02569684).

Autism spectrum disorder is associated with gut microbiota disorder in children

BackgroundThe aim of this study was to evaluate the occurrence and clinical characteristics of autism spectrum disorder (ASD) associated to the stable state of the gut microbiota.MethodsA total of 9 children with ASD and 6 healthy children used as control were selected and feces samples were collected from all of them. The 16S gene ribosomal RNA sequencing was used to analyze the difference in gut microbiota between healthy control children and ASD patients.ResultsThe results of 16S sequencing based on operational taxonomic units (OTUs) analysis showed that the ASD group and the healthy control (HC) group had a large difference in the abundance of microbiota at the level of family, genus and species. The abundance of Bacteroidales and Selenomonadales was significantly lower in the ASD group than in the HC group (p = 0.0110 and p = 0.0076, respectively). The abundance of Ruminococcaceae in the ASD group was higher than that in the HC group (p = 0.0285), while the amount of Prevotellaceae was significantly lower in the ASD group than in the HC group (p = 0.0111). The Tax4Fun analysis based on Kyoto Encyclopaedia of Genes and Genomes (KEGG) data indicated differentially expressed functional pathway between the ASD group and healthy control group associated to the nervous system, environmental information processing and cellular processing.ConclusionsThe abundance of gut microbiota in the ASD group is different from that in the healthy control children. These differences affect the biological function of the host. These results suggest that a disorder in the gut microbiota may be associated, at least in part, with ASD in children.

Mosquito control actions affect chironomid diversity in temporary wetlands of the Upper Rhine Valley.

The Upper Rhine Valley, a "hotspot of biodiversity" in Germany, has been treated with the biocide Bacillus thuringiensis var. israelensis (Bti) for mosquito control for decades. Previous studies discovered Bti nontarget effects in terms of severe chironomid abundance reductions. In this study, we investigated the impact of Bti on species level and addressed the community composition of the nontarget family Chironomidae by use of community metabarcoding. Chironomid emergence data were collected in three mosquito-control relevant wetland types in the Upper Rhine Valley. For all three sites the chironomid species composition, based on operational taxonomic units (OTUs), was different to varying degrees in the Bti-treated samples versus control samples, ranging from a significant 63% OTU reduction to an OTU replacement. We assumed that predatory chironomids are less prone to Bti than filter feeders, as the latter feed on floating particles leading to direct ingestion of Bti. However, a comparable percentage of predators and filter feeders (63% and 65%, respectively) was reduced in the Bti samples, suggesting that the feeding strategy is not the main driver for Bti sensitivity in chironomids. Finally, our data was compared to a three-year-old data set, indicating possible chironomid community recovery due to species recolonization a few years after the last Bti application. Considering the currently discussed worldwide insect decline we recommend a rethinking of the usage of the biocide Bti, and to prevent its ongoing application especially in nature protection reserves to enhance ecological resilience and to prevent boosting the current biodiversity loss.

The responding and ecological contribution of biofilm-leaves of submerged macrophytes on phenanthrene dissipation in sediments

The bacterial communities and ecological contribution of biofilm-leaves of the Vallisneria natans (VN), Hydrilla verticillata (HV) and artificial plant (AP) settled in sediments with different polluted levels of phenanthrene were investigated by high-throughput sequencing in different growth periods. There was no significant difference among the detected Alpha diversity indices based on three classification, attached surface, spiking concentration and incubation time. While Beta diversity analysis assessed by PCoA on operational taxonomic units (OTU) indicated that bacterial community structures were significantly influenced in order of attached surface > incubation time > spiking concentration of phenanthrene in sediment. Moreover, the results of hierarchical dendrograms and heat maps at genus level were consistent with PCoA analysis. We speculated that the weak influence of phenanthrene spiking concentration in sediment might be related to lower concentration and smaller concentration gradient of phenanthrene in leaves. Meanwhile, difference analysis suggested that attached surface was inclined to influence the rare genera up to significant level than incubation time. In general, the results proved that phenanthrene concentrations, submerged macrophytes categories and incubation time did influence the bacterial community of biofilm-leaves. In turn, results also showed a non-negligible ecological contribution of biofilm-leaves in dissipating the phenanthrene in sediments (>13.2%–17.1%) in contrast with rhizosphere remediation (2.5%–3.2% for HV and 9.9%–10.6% for VN).

Accounting for Bacterial Overlap Between Raw Water Communities and Contaminating Sources Improves the Accuracy of Signature-Based Microbial Source Tracking.

Microbial source tracking (MST) analysis is essential to identifying and mitigating the fecal pollution of water resources. The signature-based MST method uses a library of sequences to identify contaminants based on operational taxonomic units (OTUs) that are unique to a certain source. However, no clear guidelines for how to incorporate OTU overlap or natural variation in the raw water bacterial community into MST analyses exist. We investigated how the inclusion of bacterial overlap between sources in the library affects source prediction accuracy. To achieve this, large-scale sampling – including feces from seven species, raw sewage, and raw water samples from water treatment plants – was followed by 16S rRNA amplicon sequencing. The MST library was defined using three settings: (i) no raw water communities represented; (ii) raw water communities selected through clustering analysis; and (iii) local water communities collected across consecutive years. The results suggest that incorporating either the local background or representative bacterial composition improves MST analyses, as the results were positively correlated to measured levels of fecal indicator bacteria and the accuracy at which OTUs were assigned to the correct contamination source increased fourfold. Using the proportion of OTUs with high source origin probability, underpinning a contaminating signal, is a solid foundation in a framework for further deciphering and comparing contaminating signals derived in signature-based MST approaches. In conclusion, incorporating background bacterial composition of water in MST can improve mitigation efforts for minimizing the spread of pathogenic and antibiotic resistant bacteria into essential freshwater resources.

Optimizing body fluid recognition from microbial taxonomic profiles

In forensics the DNA-profile is used to identify the person who left a biological trace, but information on body fluid can also be essential in the evidence evaluation process. Microbial composition data could potentially be used for body fluid recognition as an improved alternative to the currently used presumptive tests. We have developed a customized workflow for interpretation of bacterial 16S sequence data based on a model composed of Partial Least Squares (PLS) in combination with Linear Discriminant Analysis (LDA). Large data sets from the Human Microbiome Project (HMP) and the American Gut Project (AGP) were used to test different settings in order to optimize performance. From the initial cross-validation of body fluid recognition within the HMP data, the optimal overall accuracy was close to 98%. Sensitivity values for the fecal and oral samples were ≥0.99, followed by the vaginal samples with 0.98 and the skin and nasal samples with 0.96 and 0.81 respectively. Specificity values were high for all 5 categories, mostly >0.99. This optimal performance was achieved by using the following settings: Taxonomic profiles based on operational taxonomic units (OTUs) with 0.98 identity (OTU98), Aitchisons simplex transform with C = 1 pseudo-count and no regularization (r = 1) in the PLS step. Variable selection did not improve the performance further. To test for robustness across sequencing platforms, we also trained the classifier on HMP data and tested on the AGP data set. In this case, the standard OTU based approach showed moderately decline in accuracy. However, by using taxonomic profiles made by direct assignment of reads to a genus, we were able to nearly maintain the high accuracy levels. The optimal combination of settings was still used, except the taxonomic level being genus instead of OTU98. The performance may be improved even further by using higher resolution taxonomic bins.

Locality or habitat? Exploring predictors of biodiversity in Amazonia

Amazonia is an environmentally heterogeneous and biologically megadiverse region, and its biodiversity varies considerably over space. However, existing knowledge on Amazonian biodiversity and its environmental determinants stems almost exclusively from studies of macroscopic above‐ground organisms, notably vertebrates and trees. In contrast, diversity patterns of most other organisms remain elusive, although some of them, for instance microorganisms, constitute the overwhelming majority of taxa in any given location, both in terms of diversity and abundance. Here, we use DNA metabarcoding to estimate prokaryote and eukaryote diversity in environmental soil and litter samples from 39 survey plots in a longitudinal transect across Brazilian Amazonia using 16S and 18S gene sequences, respectively. We characterize richness and community composition based on operational taxonomic units (OTUs) and test their correlation with longitude and habitat. We find that prokaryote and eukaryote OTU richness and community composition differ significantly among localities and habitats, and that prokaryotes are more strongly structured by locality and habitat type than eukaryotes. Our results 1) provide a first large‐scale mapping of Amazonian soil biodiversity, suggesting that OTU richness patterns might follow substantially different patterns from those observed for macro‐organisms; and 2) indicate that locality and habitat factors interact in determining OTU richness patterns and community composition. This study shows the potential of DNA metabarcoding in unveiling Amazonia's outstanding diversity, despite the lack of complete reference sequence databases for the organisms sequenced.

Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems

BackgroundMicrobial extracellular electron transfer (EET) is essential in driving the microbial interspecies interaction and redox reactions in bioelectrochemical systems (BESs). Magnetite (Fe3O4) and magnetic fields (MFs) were recently reported to promote microbial EET, but the mechanisms of MFs stimulation of EET and current generation in BESs are not known. This study investigates the behavior of current generation and EET in a state-of-the-art pulse electromagnetic field (PEMF)-assisted magnetic BES (PEMF-MBES), which was equipped with magnetic carbon particle (Fe3O4@N-mC)-coated electrodes. Illumina Miseq sequencing of 16S rRNA gene amplicons was also conducted to reveal the changes of microbial communities and interactions on the anode in response to magnetic field.ResultsPEMF had significant influences on current generation. When reactors were operated in microbial fuel cell (MFC) mode with pulse electromagnetic field (PEMF-MMFCs), power densities increased by 25.3–36.0% compared with no PEMF control MFCs (PEMF-OFF-MMFCs). More interestingly, when PEMF was removed, the power density dropped by 25.7%, while when PEMF was reintroduced, the value was restored to the previous level. Illumina sequencing of 16S rRNA gene amplicon and principal component analysis (PCA) based on operational taxonomic units (OTUs) indicate that PEMFs led to the shifts in microbial community and changes in species evenness that decreased biofilm microbial diversity. Geobacter spp. were found dominant in all anode biofilms, but the relative abundance in PEMF-MMFCs (86.1–90.0%) was higher than in PEMF-OFF-MMFCs (82.5–82.7%), indicating that the magnetic field enriched Geobacter on the anode. The current generation of Geobacter-inoculated microbial electrolysis cells (MECs) presented the same change regularity, the accordingly increase or decrease corresponding with switch of PEMF, which confirmed the reversible stimulation of PEMFs on microbial electron transfer.ConclusionThe pulse electromagnetic field (PEMF) showed significant influence on state-of-the-art pulse magnetic bioelectrochemical systems (PEMF-MBES) in terms of current generation and microbial ecology. EET was instantaneously and reversibly enhanced in MBESs inoculated with either mixed-culture or Geobacter. PEMF notably decreased bacterial and archaeal diversities of the anode biofilms in MMFCs via changing species evenness rather than species richness, and facilitated specific enrichment of exoelectrogenic bacteria (Geobacter) on the anode surface. This study demonstrates a new magnetic approach for understanding and facilitating microbial electrochemical activities.

Ecogenomics of Zooplankton Community Reveals Ecological Threshold of Ammonia Nitrogen

Communities of zooplankton can be adversely affected by contamination resulting from human activities. Yet understanding the influence of water quality on zooplankton under field-conditions is hindered by traditional labor-intensive approaches that are prone to incomplete or uncertain taxonomic determinations. Here, for the first time, an eco-genomic approach, based on genetic diversity in the mitochondrial cytochrome c oxidase I (COI) region of DNA of zooplankton was used to develop a site-specific, water quality criterion (WQC) for ammonia (NH3). Ammonia has been recognized as a primary stressor in the catchment of the large, eutrophic Tai Lake, China. Nutrients, especially NH3 and nitrite (NO3-) had more significant effects on structure of the zooplankton community than did other environmental factors. Abundances of rotifers increased along a gradient of increasing concentrations of total ammonia nitrogen (TAN), while abundances of copepods and cladocera decreased. A novel, rapid, species sensitivity distribution (SSD) approach based on operational taxonomic units (OTUs) was established to develop a WQC for NH3. The WQC based on OTUs was consistent with the WQC based on the traditional morphology taxonomy approach. This genetics-based SSD approach could be a useful tool for monitoring for status and trends in species composition and deriving ecological criteria and an efficient biomonitoring tool to protect local aquatic ecosystems in virtually any aquatic ecosystem.

Environmental and mucosal microbiota and their role in childhood asthma.

High microbial diversity in the environment has been associated with lower asthma risk, particularly in children exposed to farming. It remains unclear whether this effect operates through an altered microbiome of the mucosal surfaces of the airways. DNA from mattress dust and nasal samples of 86 school age children was analyzed by 454 pyrosequencing of the 16S rRNA gene fragments. Based on operational taxonomic units (OTUs), bacterial diversity and composition were related to farm exposure and asthma status. Farm exposure was positively associated with bacterial diversity in mattress dust samples as determined by richness (P = 8.1 × 10-6 ) and Shannon index (P = 1.3 × 10-5 ). Despite considerable agreement of richness between mattress and nasal samples, the association of richness with farming in nasal samples was restricted to a high gradient of farm exposure, that is, exposure to cows and straw vs no exposure at all. In mattress dust, the genera Clostridium, Facklamia, an unclassified genus within the family of Ruminococcaceae, and six OTUs were positively associated with farming. Asthma was inversely associated with richness [aOR = 0.48 (0.22-1.02)] and Shannon index [aOR = 0.41 (0.21-0.83)] in mattress dust and to a lower extent in nasal samples [richness aOR 0.63 = (0.38-1.06), Shannon index aOR = 0.66 (0.39-1.12)]. The stronger inverse association of asthma with bacterial diversity in mattress dust as compared to nasal samples suggests microbial involvement beyond mere colonization of the upper airways. Whether inhalation of metabolites of environmental bacteria contributes to this phenomenon should be the focus of future research.

Effect of copper on the performance and bacterial communities of activated sludge using Illumina MiSeq platforms

The anaerobic-anoxic-aerobic (A2O) process is a highly efficient sewage treatment method, which uses complex bacterial communities. However, the effect of copper on this process and the bacterial communities involved remains unknown. In this study, a systematic investigation of the effect of persistent exposure of copper in the A2O wastewater treatment system was performed. An A2O device was designed to examine the effect of copper on the removal efficiency and microbial community compositions of activated sludge that was continuously treated with 10, 20, and 40 mg L−1 copper, respectively. Surprisingly, a decrease in chemical oxygen demand (COD) and ammonia nitrogen (NH4N) removal efficiency was observed, and the toxicity of high copper concentration was significantly greater at 7d than at 1d. Proteobacteria, Bacteroidetes, Acidobacteria, Chlorobi, and Nitrospirae were the dominant bacterial taxa in the A2O system, and significant changes in microbial community were observed during the exposure period. Most of the dominant bacterial groups were easily susceptible to copper toxicity and diversely changed at different copper concentrations. However, not all the bacterial taxa were inhibited by copper treatment. At high copper concentration, many bacterial species were stimulated and their abundance increased. Cluster analysis and principal coordinate analysis (PCoA) based on operational taxonomic units (OTUs) revealed clear differences in the bacterial communities among the samples. These findings indicated that copper severely affected the performance and key microbial populations in the A2O system as well as disturbed the stability of the bacterial communities in the system, thus decreasing the removal efficiency.

Assessment of Fecal Microflora Changes in Pigs Supplemented with Herbal Residue and Prebiotic.

Antibiotic usage in animals as a growth promoter is considered as public health issue due to its negative impact on consumer health and environment. The present study aimed to evaluate effectiveness of herbal residue (ginger, Zingiber officinale, dried rhizome powder) and prebiotic (inulin) as an alternative to antibiotics by comparing fecal microflora composition using terminal restriction fragment length polymorphism. The grower pigs were offered feed containing antibiotic (tetracycline), ginger and inulin separately and un-supplemented group served as control. The study revealed significant changes in the microbial abundance based on operational taxonomic units (OTUs) among the groups. Presumptive identification of organisms was established based on the fragment length of OTUs generated with three restriction enzymes (MspI, Sau3AI and BsuRI). The abundance of OTUs representing Bacteroides intestinalis, Eubacterium oxidoreducens, Selonomonas sp., Methylobacterium sp. and Denitrobacter sp. was found significantly greater in inulin supplemented pigs. Similarly, the abundance of OTUs representing Bacteroides intestinalis, Selonomonas sp., and Phascolarcobacterium faecium was found significantly greater in ginger supplemented pigs. In contrast, the abundance of OTUs representing pathogenic microorganisms Atopostipes suicloacalis and Bartonella quintana str. Toulouse was significantly reduced in ginger and inulin supplemented pigs. The OTUs were found to be clustered under two major phylotypes; ginger-inulin and control-tetracycline. Additionally, the abundance of OTUs was similar in ginger and inulin supplemented pigs. The results suggest the potential of ginger and prebioticsto replace antibiotics in the diet of grower pig.

Comparing fungal richness and community composition in coarse woody debris in Central European beech forests under three types of management

Managing forests by selection cutting is a promising silvicultural technique for maintaining forest biodiversity. Despite the importance of fungi in decomposition and nutrient cycling in forest ecosystems, no study to date has investigated the effects of selection cutting on fungal communities, especially using a culture-independent molecular technique to assess more than just the species that are fruiting at the time of sampling. Based on operational taxonomic units (OTUs) found in coarse woody debris, we compared the richness and community composition of wood-inhabiting fungi from selection cutting, age-class, and unmanaged European beech-dominated forests. We found that fungal OTU richness in selection cutting and unmanaged forests was not significantly different (P > 0.05), but it was higher, in both cases, than that in the age-class forest (P = 0.0002). Fungal community composition was not significantly different among the three forest types (P > 0.05). Abundances of common, wood-inhabiting fungal OTUs in different forest types were significantly correlated: the highest and lowest correlations were found between unmanaged forests and selection cutting (ρ = 0.52, P < 0.0001, n = 94), and between unmanaged and age-class forests (ρ = 0.30, P = 0.0080, n = 79), respectively.

What does it take to resolve relationships and to identify species with molecular markers? An example from the epiphytic Rhipsalideae (Cactaceae)

The Cactaceae are a major New World plant family and popular in horticulture. Still, taxonomic units and species limits have been difficult to define, and molecular phylogenetic studies so far have yielded largely unresolved trees, so relationships within Cactaceae remain insufficiently understood. This study focuses on the predominantly epiphytic tribe Rhipsalideae and evaluates the utility of a spectrum of plastid genomic regions. • We present a phylogenetic study including 52 of the 53 Rhipsalideae species and all the infraspecific taxa. Seven regions (trnK intron, matK, rbcL, rps3-rpl16, rpl16 intron, psbA-trnH, trnQ-rps16), ca. 5600 nucleotides (nt) were sequenced per sample. The regions used were evaluated for their phylogenetic performance and performance in DNA-based species recognition based on operational taxonomic units (OTUs) defined beforehand. • The Rhipsalideae are monophyletic and contain five clades that correspond to the genera Rhipsalis, Lepismium, Schlumbergera, Hatiora, and Rhipsalidopsis. The species-level tree was well resolved and supported; the rpl16 and trnK introns yielded the best phylogenetic signal. Although the psbA-trnH and trnQ-rps16 spacers were the most successful individual regions for OTU identification, their success rate did not significantly exceed 70%. The highest OTU identification rate of 97% was found using the combination of psbA-trnH, rps3-rpl16, trnK intron, and trnQ-rps16 as a minimum possible marker length (ca. 1660 nt). • The phylogenetic performance of a marker is not determined by the level of sequence variability, and species discrimination power does not necessarily correlate with phylogenetic utility.

Evolutionary criteria outperform operational approaches in producing ecologically relevant fungal species inventories

Analyses of the structure and function of microbial communities are highly constrained by the diversity of organisms present within most environmental samples. A common approach is to rely almost entirely on DNA sequence data for estimates of microbial diversity, but to date there is no objective method of clustering sequences into groups that is grounded in evolutionary theory of what constitutes a biological lineage. The general mixed Yule-coalescent (GMYC) model uses a likelihood-based approach to distinguish population-level processes within lineages from processes associated with speciation and extinction, thus identifying a distinct point where extant lineages became independent. Using two independent surveys of DNA sequences associated with a group of ubiquitous plant-symbiotic fungi, we compared estimates of species richness derived using the GMYC model to those based on operational taxonomic units (OTUs) defined by fixed levels of sequence similarity. The model predicted lower species richness in these surveys than did traditional methods of sequence similarity. Here, we show for the first time that groups delineated by the GMYC model better explained variation in the distribution of fungi in relation to putative niche-based variables associated with host species identity, edaphic factors, and aspects of how the sampled ecosystems were managed. Our results suggest the coalescent-based GMYC model successfully groups environmental sequences of fungi into clusters that are ecologically more meaningful than more arbitrary approaches for estimating species richness.