Exploring the microscopic ecosystem of Cladophora algae and its diverse microbial inhabitants
In the clear, flowing waters of Nan River in northern Thailand, a remarkable green alga known locally as "Kai" or "Sa Rai Kai" thrives. For generations, local communities have harvested these filamentous green strands for both culinary and medicinal purposes, creating a unique intersection of ecology and human culture 5 .
But beyond its value as a food source, Cladophora serves as an invisible ecosystem engineer, creating microhabitats for countless microorganisms that are crucial to the river's health 1 .
Recent scientific investigations have revealed that this humble alga hosts an entire microscopic universe within its tangled filaments—a complex community of bacteria, fungi, and other microbes that may hold the key to understanding nutrient cycling in freshwater ecosystems 1 5 . As researchers from Chulalongkorn University embarked on studying these epiphytic microbiota, they uncovered a world of surprising diversity and important ecological functions, shedding new light on one of Thailand's lesser-known aquatic resources 5 .
Cladophora represents a cosmopolitan genus of filamentous green algae found in freshwater, marine, and brackish environments worldwide 1 . What makes this alga particularly remarkable is its physical structure—each filament provides an extensive surface area that serves as prime real estate for microorganisms to colonize 1 2 .
Scientists often describe Cladophora as a "microscopic forest" because its dense growth creates numerous ecological niches, much like trees in a woodland foster diverse life forms in their branches 2 6 .
This algal genus plays such a crucial role in supporting other life forms that researchers have dubbed it an "allochthonous ecological engineer" 2 .
Through its physical presence alone, Cladophora creates, modifies, and maintains habitat for countless microscopic organisms, from bacteria and archaea to protists, microalgae, fungi, and invertebrates 1 5 .
Sampling locations along the Nan River where Cladophora was studied
In the Nan River, Cladophora regularly forms conspicuous populations along river shorelines during the late growing season around March 1 8 . The local populations not only contribute to the ecosystem but have become part of the cultural and culinary heritage of northern Thailand, though their microbiological companions had remained unstudied until recently 5 .
To uncover the mysteries of Cladophora's microbial world, researchers conducted a comprehensive amplicon-based metagenomic analysis of algal samples collected from multiple sites along the Nan River 1 5 . The scientific team designed a meticulous approach to ensure their findings would be both accurate and representative of the true microbial diversity.
The research involved collecting Cladophora samples from five different locations along the Nan River across four districts—Chiang Klang (CKD), Pua (PUA), Tha Wang Pha (TD1 and TD2), and Mueang Nan District (MND) 1 8 .
Back in the laboratory, researchers employed sophisticated genetic techniques to identify the hidden residents 1 5 . They extracted genomic DNA from the algal samples after carefully washing the filaments to remove loosely associated materials.
Using Illumina MiSeq sequencing technology, they amplified and sequenced three different genetic markers:
| Research Reagent/Tool | Function in the Experiment |
|---|---|
| DNA/RNA Shield™ | Preserves nucleic acids during sample transport and storage |
| Quick-DNA™ Fecal/Soil Microbe Kits | Extracts genomic DNA from the algal microbiome |
| 341F and 805R primers | Amplifies the V3-V4 region of the 16S rRNA gene for bacterial identification |
| Reuk454FWD1 and V4r primers | Targets the V4 region of the 18S rRNA gene for eukaryotic microbe identification |
| ITS-1F and ITS-2R primers | Amplifies the Internal Transcribed Spacer (ITS) region for fungal identification |
| SILVA ribosomal RNA gene database | Reference database for taxonomic classification of sequenced organisms |
| UNITE database | Specialized reference database for identifying fungal taxa |
The investigation revealed an astonishing diversity of microbial life thriving on the Cladophora filaments from the Nan River. Genetic analysis identified a remarkable 698 bacterial genera and 575 eukaryotic genera living epiphytically on the algae 5 .
The prokaryotic community was dominated by several key bacterial phyla, with Proteobacteria being the most abundant across all sampling sites 1 8 . Other significant bacterial groups included Bacteroidetes, Cyanobacteria, and Actinobacteria 8 .
When researchers examined the eukaryotic microorganisms, they found representatives from six major supergroups: Alveolata, Amorphea, Archaeplastida, Cryptophyceae, Rhizaria, and Stramenopiles 8 .
Among these, diatoms (Stramenopiles) were particularly abundant, with species like Fragilaria and Navicula being visually dominant when examined under light microscopy 1 8 .
Perhaps most intriguing was the discovery that 227 bacterial genera were consistently present across all sampling sites 5 . These "shared taxa" represent a core microbiome that appears to have a stable relationship with Cladophora regardless of slight variations in river conditions at different locations.
| Taxonomic Group | Representative Genera | Relative Abundance/Notes |
|---|---|---|
| Bacteria (Prokaryotes) | ||
| Proteobacteria | Methylotenera, Rhodobacter | Most abundant phylum across all sites |
| Bacteroidetes | Flavobacterium, Terrimonas | Involved in organic matter decomposition |
| Cyanobacteria | Unclassified genera | Contributes to photosynthetic activity |
| Eukaryotes | ||
| Diatoms (Stramenopiles) | Fragilaria, Navicula | Visually dominant under microscopy |
| Ciliates (Alveolata) | Vorticella | Predatory microorganisms |
| Fungi | Penicillium, Candida | Most diverse in decomposition |
When researchers delved deeper into the functions of these microbial residents, they discovered that many play crucial roles in nutrient cycling and other ecological processes 1 . Through functional inference based on the identified taxa, scientists determined that Cladophora's microbiome contains organisms capable of participating in nitrogen cycling, phosphorus accumulation, sulfur reduction, and degradation of various organic compounds 1 8 .
Among the most significant findings was the identification of 17 core bacterial genera that appear consistently in Cladophora microbiomes across different geographic locations, including previous studies in the United States 5 . These core taxa include:
The fungal community, successfully sequenced from the TD1 site, was dominated by Ascomycota (53.96%) and Chytridiomycota (29.95%), with genera like Penicillium and Candida among the most abundant 8 .
Many of these fungi function as decomposers, breaking down organic matter and contributing to nutrient recycling in the river ecosystem 8 .
| Ecological Function | Specific Process | Representative Bacterial Genera |
|---|---|---|
| Nutrient Cycling | Denitrification | Acidovorax, Methylotenera |
| Nitrogen fixation | Unclassified genera | |
| Ammonium oxidation | Unclassified genera | |
| Polyphosphate accumulation | Unclassified genera | |
| Sulfate reduction | Unclassified genera | |
| Biosynthesis | Vitamin production | Cobalamin (B12) biosynthesis |
| Degradation | Cellulose degradation | Unclassified genera |
| Degradation of aromatic compounds | Unclassified genera | |
| Chitin degradation | Unclassified genera |
The Nan River represents a lotic (flowing water) ecosystem, which presents unique challenges compared to the lentic (still water) environments where Cladophora has been more extensively studied 1 . In these flowing systems, the unidirectional water movement creates distinct patterns of nutrient availability and microbial distribution.
In lotic environments, nutrients arrive as pulses from the adjacent floodplain, typically during seasonal rainfall, rather than the more consistent seasonal turnover seen in lakes 1 . This means that Cladophora and its microbial community must be adapted to periods of feast and famine in terms of resource availability.
Additionally, nutrients in flowing systems are less recyclable due to the constant downstream movement of water, unlike in lakes where sedimentation allows for more localized recycling 1 .
The flowing nature of the river also means that microbial communities must have strategies to remain associated with the algal filaments despite the constant force of water movement.
This likely contributes to the prevalence of bacteria like Terrimonas that produce extracellular polymeric substances—these sticky secretions help create a protective biofilm that anchors the microbial community to the Cladophora filaments 5 .
Lotic ecosystem with unidirectional flow
Biofilm formation for attachment
Adapted nutrient cycling strategies
The exploration of Cladophora's epiphytic microbiota in the Nan River has revealed an unexpectedly complex microscopic ecosystem thriving within what appears to the naked eye as simple green algae. This research has illuminated the crucial ecological roles played by these microbial communities, from driving nutrient cycles that support river health to potentially enhancing the growth of their algal host through vitamin production and other mutualistic interactions 1 5 .
The discovery of a core microbiome that remains consistent across different geographic locations suggests that Cladophora fosters specific, stable relationships with certain microbial partners 5 . These relationships have likely evolved over long periods, resulting in specialized functional partnerships that contribute significantly to freshwater ecosystem functioning.
As these microbial communities include organisms involved in everything from nitrogen cycling to cellulose degradation, they serve as invisible engines that power the river's ecological processes 1 8 .
For the local communities of northern Thailand who have long valued Cladophora as "Kai," this research adds a new dimension of appreciation—what was traditionally seen simply as a food source is now recognized as a living ecosystem in its own right, hosting a diverse community of microscopic inhabitants that contribute to the health of the Nan River.
As research continues, scientists hope to further unravel the complex relationships between Cladophora and its microbiota, potentially revealing new insights about freshwater ecology and the invisible networks that sustain our planet's aquatic resources.
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